Entertainment. Gianluca On Thu, 31 May 2012, Kapil jain wrote: > Hi all, > I am running md simulation on homology model of a membrane protein, following the membrane > protein tutorial. E-mail: [email protected],. uiuc. From: Gianluca Interlandi (gianluca_at_u. Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. washington. Languages spoken: English. Comparative controls consisted of FocH (high affinity with and. washington. > Le 2015-07-16 17:20, Gianluca Interlandi a écrit : >> Also, apropos documentation. Gianluca Interlandi Curriculum Vitae Department of Bioengineering, University of Washington, 1705 NE Pacific Street, 98195 Seattle, WA, [email protected]> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on small On Wed, 16 Sep 2020 at 11:40, Gianluca Interlandi <gianluca_at_u. edu > Subject: Re: namd-l: DCD > > Load your psf+dcd into VMD. Just source the Tcl file and use the 'unwrap' procedure. edu> Date: Monday, May 7, 2007 7:26 pm Subject: Re: namd-l: query about wrapped coordinates > I have actually found a much easier way of adding the crystal > information > to your trajectory. (2010) The catch bond mechanism between von Willebrand factor and platelets investigated by molecular dynamics simulations. washington. From: Gianluca Interlandi (gianluca_at_u. 7 out the door on Friday. Biochemistry. mx: "Re: Fat node" Previous message: Dan Strahs: "checkpoint software for NAMD?" In reply to: Dan Strahs: "checkpoint software for NAMD?". washington. washington. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). washington. Next in thread: Gianluca Interlandi: "Re: NAMD 2. 6 : Tue Dec 27 2016 - 23:21:14 CST Gianluca Interlandi's 67 research works with 730 citations and 2,578 reads, including: Rate limiting step of the allosteric activation of the bacterial adhesin FimH investigated by molecular. prm". 7 out the door on Friday. From: Gianluca Interlandi (gianluca_at_u. washington. , "not. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. 97 pN*nm = 1 Kcal/molOn Wed, Nov 26, 2014 at 04:06:03PM -0800, Gianluca Interlandi wrote: > Dear vmd list, > > I noticed that I get slightly different results when I measure the > distance between two atoms using "measure bond" vs by measuring the length > of the vector between the two atoms. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. washington. Re: query about wrapped coordinates. Best, Jerome Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit : Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. Spaces. I doubt that there is a way to haveReply: Gianluca Interlandi: "Re: NAMD timestep and numsteps" Messages sorted by: [ attachment ] Hi NAMD users, I was running a simulation using NAMD with timestep 5 fs and numsteps 5000. Reply: Gianluca Interlandi: "Re: Changing Boundary conditions from PBC to non-periodic" Messages sorted by: [ attachment ] Dear NAMD users, A portion of my protein is outside of the simulation box. Gianluca Interlandi 1 , Minhua Ling, An Yue Tu, Dominic W Chung, Wendy E Thomas Affiliation 1 Department of Bioengineering, University of Washington, Seattle, Washington, United States of America. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi < gianluca_at_u. washington. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" Previous message: L. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. washington. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. washington. Next in thread: Gianluca Interlandi: "Re: NAMD 2. Eddie: "gentoo ebuild" Previous message: Robert Johnson: "Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes" Maybe in reply to: Norman Geist: "AW: AW: Running NAMD on Forge (CUDA)" Complex between VWF A1 and GpIbα and amino acid sequence of the A1 domain. edu> > wrote: > are other people also using those GPUs? > > Previous message: Gianluca Interlandi: "Conversion for forces" In reply to: Gianluca Interlandi: "Conversion for forces" Next in thread: Gianluca Interlandi: "SMD and restart" Reply: Gianluca Interlandi: "SMD and restart" Messages sorted by: [ attachment ] This archive was generated by Research Assistant Professor gianluca@u. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. Display options Format Abstract The bacterial adhesin FimH is a model for the study of protein allostery because its structure has been resolved. 7 released" Messages sorted by: [ attachment ] Hi all, I pushed 2. edu>> > > I suspect that E3_19 might not be stable with this type of > implicit solvent model (it doesn't contain a term to take the > non-polar solvation energy into accout). 15 K 1 KT = 2. Gianluca Interlandi [email protected] orcid. washington. edu) Date: Thu Apr 07 2011 - 13:57:41 CDT Next message: Axel Kohlmeyer: "Re: Abe versus Lincoln" Previous message: Gianluca Interlandi: "Re: Abe versus Lincoln" In reply to: Axel Kohlmeyer: "Re: Abe versus Lincoln"From: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. Sokurenko 1 , *. Search 214,979,228 papers from all fields of science. edu> > wrote: > Roy, > > I think that you are confusing two things. edu]Reply All Saturday,. edu) Date: Wed May 06 2009 - 11:04:21 CDT Next message: Anton Arkhipov: "Re: Langevin damping coefficient" Previous message: Benjamin Stauch: "diffusion / fex peptide problem" In reply to: Anton Arkhipov: "Re: Langevin damping. On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi < gianluca_at_u. edu> wrote: >> blades generally tend to be a bit slower than "normal" nodes. at 298. washington. 7 with the PLUMED patch" Messages sorted by: [ attachment ] Hi Gianluca, My guess is that something went wrong while patching namd with plumed. Gianluca, Looking at the code, it does not, but that would be easy to adapt from the NAMD's ComputeCrossterms. This school has it's > own biophysics division. uiuc. The otherGianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. I thought I will see in my output file the energies stored at times 0 fs, 500 fs,. The more tasks you have the > more frequently the CPUs need to update each other about the position > of Next message: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Previous message: Gianluca Interlandi: "Re: Jarzinsky's equation" Next in thread: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Reply: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Reply: Axel Kohlmeyer: "Re: Fwd: Installing NAMD on windows" Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. washington. edu> wrote:From: Gianluca Interlandi (gianluca_at_u. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. , and Thomas W. edu) Date: Tue Sep 15 2020 - 20:34:44 CDT Next message: Kodituwakku,Dimuthu Nirmani: "Re: Post processing NAMD trajectory" Previous message: Victor Zhao: "Re: Re: AMBER input and REST2 leads to crash" Next in thread:. edu> > wrote: > are other people also using those GPUs? > >> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. washington. Gianluca Interlandi Research Assistant Professor. washington. edu> wrote: > Hi Fatemeh, > From: Gianluca Interlandi (gianluca_at_u. Gianluca has 2 jobs listed on their profile. washington. In the NAMD folder that you downloaded there >> is a file called "notes. VMD-L Mailing List. Education/training Institution and location Dates attended Degree Conferred Field of study Interlandi G, Thomas WE. The simulations were not performed at constant velocity > but at constant force. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. edu> wrote: In reply to: Gianluca Interlandi: "Compiling NAMD 2. washington. edu> wrote: >> Hi! >> >> Are there any benchmarks available which compare the performance of NAMD on >> Lincoln (CUDA heterogenous cluster) with its performance on a traditionalVMD-L Mailing List. washington. washington. Facebook gives people. At the point of breaking the temperature raises of a few> Auftrag von Gianluca Interlandi > Gesendet: Sonntag, 27. In the text field you can enter your atom selection, e. SASA in NAMD is used internally > to perform simulations in implicit solvent, whereas SASA in VMD is used to > analyse trajectories. I have a new computer that came with Windows 10, which uses UEFI with a disk that has a GPT label. washington. . washington. washington. washington. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. Previous message: Gianluca Interlandi: "stepspercycle" In reply to: Gianluca Interlandi: "stepspercycle" Next in thread: Gianluca Interlandi: "Re: AW: stepspercycle" Reply: Gianluca Interlandi: "Re: AW: stepspercycle" Messages sorted by: [ attachment ] No idea where you were looking, but this parameter is still fundamental for. edu Phone: (206)685-4435 Office: Foege N430 E Gianluca Interlandi I am interested in understanding at molecular level the function of proteins involved in hemostasis and thrombosis, and how they interact with each other and with material surfaces. >> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. washington. Anton. From: Gianluca Interlandi (gianluca_at_u. Proteins 78, 2506–2522 [PMC free article] [Google Scholar] > On Wed, 16 Sep 2020 at 11:40, Gianluca Interlandi <gianluca_at_u. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. Reply: Gianluca Interlandi: ""wrapAll on" with a complex" Reply: Gianluca Interlandi: "Scale" Messages sorted by: [ attachment ] Dear NAMD users, I'm performing SMD simulations and I have problems when I restart a simulation, i. edu] Sent: Thursday, April 05, 2012 5:04 PM To: Buddhadev Maiti Cc: Jérôme Hénin; namd-l_at_ks. What can be the possible cause for this or does it happens naturallyOn Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. edu) Date: Thu Mar 17 2011 - 17:58:46 CDT Next message: Giacomo Fiorin: "Re: GBIS and ABF" Previous message: Branko: "GBIS and ABF" In reply to: Gianluca Interlandi: "Re: NAMD 2. I also ran a non-CUDA job on Forge > using 16 CPUs. 3 hours/ns (stepsize 1, fullElectFrequency 1 and stepspercycle 20). C; the more troublesome part is the lack of long-range electrostatic treatments. > > > > Forget about creating a pdb file. Cancellation policy. m. One of the two proteins has reached one of > the boundaries of the box and it has been wrapped around. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. edu) Date: Tue Oct 31 2023 - 21:41:13 CDT Next message: Vasista: "STRIDE breaks after 100,000 protein atoms" Previous message: Victor Kwan: "Re: VMD openGL over ssh from a server with NVIDIA" In reply to: Victor Kwan: "Re: VMD openGL over ssh from a server with NVIDIA". washington. Living Room. From: Gianluca Interlandi [gianluca_at_u. Best, Jerome Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit :Reply: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi <gianluca_at_u. Reply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] have you tried the multicore build? I wonder if the prebuilt smp one is just not working for you. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" From: Gianluca Interlandi (gianluca_at_u. 7 with the PLUMED patch" In reply to: Gianluca Interlandi: "Compiling NAMD 2. Previous message: Gianluca Interlandi: "Re: Compiling NAMD 2. SASA in NAMD is used > internally to perform simulations in implicit solvent, whereas SASA in > VMD is used to analyse trajectories. washington. In reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. washington. by G. e. Member since 2014. If I > want to use all 6 CUDA devices in a node, how many processes is it > recommended to spawn?> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. Swett wrote: > From your email, it's apparent that you are in > the pharmacy school of the university of maryland. UW Bioengineering announces that Barry Lutz is hired as tenure-track faculty, Gianluca Interlandi joins faculty and Suzie Pun is promoted to full professorIn reply to: Gianluca Interlandi: "NAMD + nice" Messages sorted by: [ attachment ] Nice (process priority) is only supported in NET version of Charm++. October 10, 2019 - Present·Syracuse, Italy Da Host fai da te a Imprenditore Extra Alberghiero Owner and Founder at Baroque Apartments Syracuse, Italy Agenzia di affitti. On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi < gianluca_at_u. Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of HealthRe: NAMD 2. I'm testing specifically this protein for its beaviour. Author Profile. edu) Date: Tue Oct 17 2006 - 00:36:56 CDT Next message: Jacob Poehlsgaard: "Intel Woodcrest version?" Previous message: Jim Phillips: "Free Linux Cluster-Building Workshop - 30 Nov 2006 - 01 Dec 2006" In reply to: Gianluca Interlandi: "SMD and restart"> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. ca) Date: Tue Oct 31 2023 - 20:31:14 CDT Next message: Gianluca Interlandi: "Re: VMD openGL over ssh from a server with NVIDIA" Previous message: Victor Kwan: "Re: VMD openGL over ssh from a server with NVIDIA" In reply to: Gianluca Interlandi: "Re: VMD openGL over ssh from a. I know the lack of treatment of the hydrophobic part but the point here is the different results for same implicit solvent model. Previous message: Gianluca Interlandi: "NAMD 2. Policies. edu> wrote: >> blades generally tend to be a bit slower than "normal" nodes. . My laboratory combines tools from computational structural biology, like molecular dynamics simulations and Monte Carlo methods, with biochemical and biophysical assays to unravel the molecular basis behind biological processes like the blood coagulation cascade and cellular adhesion. Anderson: "Re: rlwrap problem on" In reply to: Frank Barry: "rlwrap problem on" Next in thread: Gianluca Interlandi: "Re: rlwrap problem on" Reply:. edu, Tel: (206) 685 4435, Fax: (206) 685 3300 1. I > attach a plot of a constant velocity simulation where I'm pulling two > proteins apart. 7 released". It's > slightly faster but still not that much faster than running on 16 CPU cores. Next in thread: Gianluca Interlandi: "Re: namd-l: DCD for windows" Messages sorted by: [ attachment ] Hi, We don't have a build of catdcd for windows currently, but it should be possible to make one. 7b1 on Abe" Previous message: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" In reply to: Gianluca Interlandi: "Re: Yet another. Next in thread: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 5:21 PM, Gianluca Interlandi <gianluca_at_u. washington. " Messages sorted by: [ attachment ] On Sun, 2009-08-30 at 12:11 -0700, Gianluca Interlandi wrote: > Thank you Mike for sharing your information. 7b1 - effects of configuration parameters and hardware. 7 released. You should simulate it in explicit water (or try one of the implicit From: Gianluca Interlandi <gianluca_at_u. edu> wrote: > Hi Fatemeh, >> On Wed, Dec 12, 2012 at 12:26 PM, Gianluca Interlandi <gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. In this way, you could get a feeling what NAMD can do before you > invest money. edu) Date: Fri May 04 2007 - 17:53:42 CDT Next message: Lechuga, Javier: "Simulating air with NAMD" Previous message: Gianluca Interlandi: "Re: query about wrapped coordinates" Maybe in reply to: Gianluca Interlandi: "Re: query about wrapped coordinates" INVENTING THE FUTURE OF MEDICINE. We are building a smaller cluster though in the lab and will test the scalability2006/9/6, Gianluca Interlandi <gianluca_at_u. washington. 7b1 on NCSA Abe. edu) Date: Thu Nov 02 2006 - 15:40:40 CST Next message: Gianluca Interlandi: "Re: SMD on center of mass" Previous message: Ugur Akgun: "ABF on a single molecule" In reply to: Gianluca Interlandi: "Re: external force" Next in. PMID: 33550613 PMCID: PMC8089038 DOI: 10. The other> Auftrag von Gianluca Interlandi > Gesendet: Sonntag, 27. 6 ns/day for a 100k atom system with roughly those same parameters (and. I'm testing specifically this protein for its beaviour. washington. Gianluca Interlandi. From: Victor Kwan (vkwan8_at_uwo. washington. washington. 6 version, although I am not running the cluster at full load yet. > > > > I have already run a bunch of pulling simulations in the NVE ensemble. washington. Previous message: Gianluca Interlandi: "Re: tools for Charmm" In reply to: Gianluca Interlandi: "Re: Charmm" Messages sorted by: [ attachment ] On 02/20/2014 01:10 PM, Gianluca Interlandi wrote: > I usually use the CHARMM program itself to generate a CHARMM PSF file. edu) Date: Wed Oct 20 2010 - 15:33:33 CDT Next message: jnsong: "how to cenvert NAMD binary coordinate file to text file" Previous message: Jim Phillips: "Re: NAMD 2. I'm > not sure whether the CHARMM program can read. washington. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. washington. Michel Espinoza-Fonseca: "Re: Vibrational. edu on behalf of Gianluca Interlandi [gianluca_at_u. A 1 TB > Samsung Evo 850 Pro costs 470$, a 1 TB Intel costs ~ 600$ and a PCIe Intel > 1 TB is over 2000$. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on small> 2011/6/29 Gianluca Interlandi <gianluca_at_u. washington. washington. >> >> i am attaching some graphs with performance numbers from. Abstract. During the minimization and equilibriation with protein constrained, the > disulfide bond breaks. edu] > Sent: Thursday, April 05, 2012 5:04 PM > To: Buddhadev Maiti > Cc: Jérôme Hénin; namd-l_at_ks. SASA in NAMD is used > internally to perform simulations in implicit solvent, whereas SASA in > VMD is used to analyse trajectories. From: Gianluca Interlandi (gianluca_at_u. 7 On Wed, Sep 18, 2013 at 11:43:49AM -0700, Gianluca Interlandi wrote: > Dear VMD list, > > I think that this question was asked previously. I got 0. Biochemistry. edu. 7 with the PLUMED patch. edu) Date: Thu Apr 09 2015 - 17:39:49 CDT Next message: Gianluca Interlandi: "Re: measure sasa not consistent" Previous message: John Stone: "Re: measure sasa not consistent" Next in thread: Gianluca Interlandi: "Re: measure energy"> From: Gianluca Interlandi [gianluca_at_u. Re: replica exchange and GPU acceleration. 7 released" Messages sorted by: [ attachment ] Dear Jim, Do you happen to have the. , "not. I am > using the option "wrapAll on". edu > <mailto:gianluca_at_u. From: Buddhadev Maiti (bmaiti_at_gsu. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. washington. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. edu] Sent: Monday, June 20, 2016 12:46 PM To: Richard Wood Cc: John Stone; vmd-l_at_ks. washington. Policies. From: Gianluca Interlandi (gianluca_at_u. Thanks for the reply. edu) Date: Thu Mar 17 2011 - 17:58:46 CDT Next message: Giacomo Fiorin: "Re: GBIS and ABF" Previous message: Branko: "GBIS and ABF" Messages sorted by: [ attachment ] Dear Jim, Do you happen to have the charmm++. Gianluca From: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. washington. washington. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. MyOne Bedroom Apartment, Sleeps 3 - C$150 avg/night - Ortigia - Amenities include: Internet, Air conditioning, TV, Satellite or cable, No smoking Bedrooms: 1 Sleeps: 3 Minimum 2 night(s) stay Bookable directly online - Book vacation rental 11131246 with Vrbo. Reply: Gianluca Interlandi: "Re: Jarzinsky's equation" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] By having the force and the extension that the force is applied to you can> 2011/6/29 Gianluca Interlandi <gianluca_at_u. Previous studies. I empolyed PBC condition with wraping water and wraping all options on. edu) Date: Thu Apr 05 2012 - 16:30:29 CDT Next message: Gianluca Interlandi: "RE: DCD" Previous message: Axel Kohlmeyer: "Re: DCD" In reply to: Buddhadev Maiti: "RE: DCD" Next in thread: Gianluca Interlandi: "RE: DCD" Reply: Gianluca Interlandi: "RE: DCD". View Gianluca Interlandi’s profile on LinkedIn, the world’s largest professional community. 6 ns/day for a 100k atom system with roughly those same parameters (and. From: Gianluca Interlandi (gianluca_at_u. washington. From: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. edu) Date: Thu Feb 20 2014 - 13:15:51 CST Next message: zeynab mohamad hoseyni: "FATAL ERROR: EOF ENCOUNTERED READING CROSS-TERMS FROM PSF FILE" Previous message: Kenno Vanommeslaeghe: "Re: tools for Charmm" In reply to: Kenno Vanommeslaeghe: "Re:. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build?Next in thread: Gianluca Interlandi: "Re: NAMD 2. Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. edu) Date: Wed Jul 16 2014 - 00:32:49 CDT Next message: Sadegh Faramarzi Ganjabad: "Re:Subject: Re: Subject: Re:Re: New partial charges after patching" Previous message: Gianluca Interlandi: "Re: Force field design" Next in. My> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. edu) Date: Mon Apr 11 2011 - 14:41:28 CDT Next message: Axel Kohlmeyer: "Re: Help building a desktop for namd" Previous message: Buddhadev Maiti: "(no subject)" In reply to: Axel Kohlmeyer: "Re: Help building a desktop for namd" Next in. edu) Date: Wed May 16 2007 - 14:43:41 CDT Next message: Ayşe Özlem Sezerman: "System charge" Previous message: Peter Freddolino: "Re: Minimization" In reply to: Viswanadham Sridhara: "How to unsubscribe ?" Messages. Bioengineering. On Thu, Apr 7, 2011 at 2:22 PM, Gianluca Interlandi <gianluca_at_u. Eric Klavins Professor. Stenkamp, 3 Wendy E. washington. Chemistry. washington. washington. Reply: Gianluca Interlandi: "Re: Abe versus Lincoln" Messages sorted by: [ attachment ] Hi Gianluca, Using 4 Lincoln nodes with a 112580 atoms system I get 9. What this rental offers. uiuc. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. 20-23 2012)<br><br>2001 May/2002 September: Master in Tourism Management - Academy of Trade and Tourism, Trento, Italy (1900 hrs). Gianluca Interlandi 1 Affiliation 1 Department of Bioengineering, University of Washington, Seattle, Washington, USA. uiuc. edu> wrote: > Hi Fatemeh, > > Thanks for replying. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"From: Gianluca Interlandi (gianluca_at_u. Specifically, I’m testing different binding domains. washington. 26588 Item in Clipboard Cite. Search for: Main Menu. <br> <br>1999 March: Degree in modern languages result 107/110 - University of Catania, Italy with a degree thesis on Irish. In reply to: Gianluca Interlandi: "Re: Question about equilibration" Next in thread: Gianluca Interlandi: "Re: Question about equilibration" Reply: Gianluca Interlandi: "Re: Question about equilibration" Messages sorted by: [ attachment ] Because an X-ray is assumed to be a structure at "zero K" and an MD equilibrated. edu, Tel: (206) 685 4435, Fax: (206) 685 3300 1. washington. unam. edu) Date: Wed May 06 2009 - 11:04:21 CDT Next message: Anton Arkhipov: "Re: Langevin damping coefficient" Previous message: Benjamin Stauch: "diffusion / fex peptide problem" In reply to: Anton Arkhipov: "Re: Langevin damping coefficient" Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. uiuc. edu Search for more. washington. washington. Gianluca has 2 jobs listed on their profile. From: Gianluca Interlandi (gianluca_at_u. Re: Vibrational mode analysis. 1. Interlandi Mortgage Consultants, LLC Dec 2008 - Present 14 years 3 months. Gianluca Interlandi Research Assistant Professor. Next in thread: Gianluca Interlandi: "Re: Should you cap C and N termini?" Reply: Gianluca Interlandi: "Re: Should you cap C and N termini?" Messages sorted by: [ attachment ] We generally use caps because our systems are individual domains within larger proteins. gov) Date: Fri Jun 18 2004 - 14:48:36 CDT Next message: Gianluca Interlandi: "Re: recentering protein in the waterbox" Previous message: Jerry Ebalunode: "recentering protein in the waterbox" Messages sorted by: [ attachment ] Hello, I'm running namd and am getting the following errors as itsIn reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. edu> wrote: > Dear all, > > Does anybody have experience simulating carbohydrates with NAMD? In > particular, I'm interested whether the CHARMM or the AMBER force field is > more accurate to simulate carbohydrates. You should simulateCorresponding Author. At some point there will be a web page here. > On Thu, Dec 2, 2010 at 2:35 PM, Gianluca Interlandi <gianluca_at_u. edu) Date: Wed Jul 16 2014 - 00:32:49 CDT Next message: Sadegh Faramarzi Ganjabad: "Re:Subject: Re: Subject: Re:Re: New partial charges after patching" Previous message: Gianluca Interlandi: "Re: Force field design" Next in. edu> Date: Monday, May 7, 2007 7:26 pm Subject: Re: namd-l: query about wrapped coordinates > I have actually found a much easier way of adding the crystal > information > to your trajectory. washington. washington. washington. There have been over 180 downloads and no complaints so far. View all 11 amenities. 7 ns/day, which seems decent given the system size. washington. > Auftrag von Gianluca Interlandi > Gesendet: Freitag, 13. From: Axel Kohlmeyer (akohlmey_at_gmail. Rooms and beds. washington. edu]Reply All Saturday,. 2016. 7b1 on Abe" Previous message: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" In reply to: Gianluca Interlandi: "Re: Yet another. You should simulate it in explicit water (or try one of the implicitIn reply to: Gianluca Interlandi: "What, if no temperatue control specified?" Messages sorted by: [ attachment ] Hi! A technical question. washington. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. The simulations were not performed at constant velocity > but at constant force. Interlandi G. I know the lack of treatment of the hydrophobic part but the point In reply to: Gianluca Interlandi: "Conversion for forces" Messages sorted by: [ attachment ] Gianluca, kcal/mol is an energy so kcal/mol/A should be a force kcal/mol/A^2 is probably a force constant for a spring. Hi I’m Yiming Li, and I’m a senior in bioengineering. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. On Thu, Oct 20, 2011 at 05:48:32PM -0700, Gianluca Interlandi wrote: > Dear VMD users, > > A while ago I bothered this list asking for recommendations for a > lightweight laptop to buy which would support a decent 3D acceleration in > order to use VMD in presentations. washington. Gianluca Interlandi Curriculum Vitae Department of Bioengineering, University of Washington, 1705 NE Pacific Street, 98195 Seattle, WA, [email protected] on Abe" In reply to: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" Messages sorted by: [ attachment ] The amount of computational work that you have for the nonbonded short-range interactions (which is the dominant part of the overallConvert solvated CHARMM PDB + PSF to Amber. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. I was getting 2. washington. Gianluca Interlandi Curriculum Vitae Department of Bioengineering, University of Washington, 1705 NE Pacific Street, 98195 Seattle, WA, [email protected]: Gianluca Interlandi (gianluca_at_u. The read speed of the trajectory will go much faster if you select the "load all at once" checkbox in the moleculeRe: Vibrational mode analysis. There have been over 180 downloads and no complaints so far. > You could build a PC with the Asus p5Q Pro Motherboard, Intel Quadcore Q8200 > and two GTX 285 cards for under 900$ (plus the cost of the usual PC > components). 6 version, although I am not running the cluster at full load yet. washington. washington. 7b1 on NCSA Abe. washington. In reply to: Gianluca Interlandi: "Re: Changing Boundary conditions from PBC to non-periodic" Messages sorted by: [ attachment ] How would somebody want to simulate explicit water molecules without PBC? The water molecules will quickly diffuse and your protein be in vacuum. Re: Does Berendsen increase viscosity of water? From: Gianluca Interlandi (gianluca_at_u. edu) Date: Wed Jun 15 2011 - 14:18:43 CDT Next message: Reichert, David: "RE: Question about equilibration" Previous message: Richard Wood: "Re: Question about equilibration" In reply to: Richard Wood: "Re: Question about. 122076 s/step, which is 16% slower than using > the 6Re: Question about equilibration. 0 and 2. Bioengineering. 478 KJ/mol = 0. From: Gianluca Interlandi <gianluca_at_u. washington. The Netherlands) is an antibody raised against K12 FimH-lectin domain (residues 1–160) and previously determined to recognize or induce the high affinity state of K12 FimH, especially in the presence of ligand ( buffer in wells of 96-well flat-bottom plates at 37 °C for 1 h. edu) Date: Mon May 28 2007 - 10:33:29 CDT Next message: Gianluca Interlandi: "Re: Protein in/out of box" Previous message: Peter Freddolino: "Re: constraints on zinc ions" In reply to: Monika Sharma: "Protein in/out of box" Next in. edu]Reply All Saturday,. NAMD doesn't that i know of. Here they are: a. washington. edu) Date: Thu Jul 16 2015 - 16:20:34 CDT Next message: Simon Kit Sang Chu: "Minimization without MD" Previous message: Gianluca Interlandi: "Re: namd ibverbs" In reply to: Gianluca Interlandi: "Re: namd ibverbs" Next in thread: Maxime Boissonneault: "Re: namd ibverbs" The bacterial adhesin FimH is a model for the study of protein allostery because its structure has been resolved in multiple configurations, including the active and the inactive state. 1 on it using Legacy Bios and a. Electrical. 100% refund of amount payable if you cancel at least 14 days before check-in. 26588. edu> wrote: >> if you want to go low risk and don't have much experience with GPU, then >> probably the best deal you can currently get for running. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. NAMD supports CHARMM22 parameter files. From: Gianluca Interlandi (gianluca_at_u. edu) Date: Tue Nov 01 2011 - 14:14:51 CDT Next message: Gianluca Interlandi: "Re: rlwrap problem on" Previous message: Joshua A. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. washington. I needed to install the 'patch' program. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. washington. From: Gianluca Interlandi (gianluca_at_u. washington. unizh. In the text > field you can enter your atom selection, e. edu> > wrote: > are other people also using those GPUs? > > From: Gianluca Interlandi (gianluca_at_u.