RE: [gmx-users] Re: dimer simulation

Try to maximize the intra- and inter-peptide hydrophobic interactions? I guess it can share the same parameters, just guess, no much idea. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Vitaly Chaban [vvcha...@gmail.

[gmx-users] Re: dimer simulation

I think your choice should depend on what bonds you expect between the two monomers forming a dimer. -- Dr. Vitaly Chaban > Dear gmx-users > I want to simulate a protein which biological function defined by dimer > formation. I need to simulate this protein in dimer as well as in > monomeric for

[gmx-users] dimer simulation

Dear gmx-users I want to simulate a protein which biological function defined by dimer formation. I need to simulate this protein in dimer as well as in monomeric form to solve my objectives. I am using Gromacs-4.0.4 for simulation. I have a doubt, is there any specific parameters for dimer simulat

Re: [gmx-users] New beta release: 4.5-beta3

- Original Message - From: Da-Wei Li Date: Wednesday, August 11, 2010 6:23 Subject: Re: [gmx-users] New beta release: 4.5-beta3 To: Discussion list for GROMACS users > Hi,all > > Unfortunately, it still crash. Here it is the output of mdrun. Both > Gromacs-4.0.7 and non-parallel 4.5b3

[gmx-users] Error while trying free energy calculation

Hi There, I was trying to run a free energy tutorial given at "* http://www.dillgroup.ucsf.edu/group/wiki/index.php?title=Free_Energy:_Tutorial *" While trying the very first run i.e. mdrun using "*min_lbfgs0.mdp*" I ended up with following error ERROR: With coulombtype = P

[gmx-users] pulling simulation with implicit solvent

Hi all, Can anyone please give me a mdp file for running pulling simulations in implicit solvent using GROMACS? Thanks in advance Samrat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www

[gmx-users] Re: pulling simulation using implicit solvent in GROMACS

Please keep all Gromacs-related correspondence on the gmx-users list. Implicit solvent is available in the current 4.5 beta release. Another tip: the mailing list search would have turned this same answer up in a few seconds. This same question has been asked dozens of times. -Justin Samra

Re: [gmx-users] New beta release: 4.5-beta3

Hi,all Unfortunately, it still crash. Here it is the output of mdrun. Both Gromacs-4.0.7 and non-parallel 4.5b3 work fine on this system. I use mvapich2 and intel compiler. *** Getting Loaded... Reading file em.tpr, VERSION 4.5-beta3 (single precision) Loaded with Money

Re: [gmx-users] GMXRC missing

Hi Ondrej, I can confirm the problem. We'll fix it for the next release (unfortunately it didn't make it in -beta3). Rossen On 08/10/2010 04:13 PM, Ondrej Marsalek wrote: Dear all, I have installed 4.5 beta2 using cmake and it seems that the GMXRC files are missing in the installation. Can

[gmx-users] New beta release: 4.5-beta3

New beta release of gromacs is available for testing: ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5-beta3.tar.gz. Many bugs have been fixed in this release, mainly double precision support with icc compilers, SSE2. Have a look at the release note on the website for more details. There are st

Re: [gmx-users] Mix two solvents

dear Rob, you can manually edit one of the gro file to increase the length in one direction by an arbitrary amount, then use genbox: genbox -cp -cs (I just did that with water and methanol from the gromacs tutorials, works just fine) maybe set -vdwd to an adequate value to prevent insertion o

[gmx-users] gromacs-4.5-beta2 implicit solvent lincs errors

Hello. I have tested GBSA in 4.5 beta2 on 3 different machines: OSX 10.6 w/ core2duo, Centos5.5 w/ dual socket quad core Xenon, and another Linux machine (unsure of OS) w/ quad socket hexacore AMD Istambul. I tested the same tpr on all machines and only the core2duo runs the job successfully. Th

Re: [gmx-users] Reduced Units

On Mon, Aug 9, 2010 at 9:58 AM, wrote: > Hi, > > I want to use the pme algorithm in GROMACS. Thge size of my box is > 8.2x8.2x8.2 in reduced units. I am considering a collection of 1000 > of CO2 molecules. If I am using reduced units, the values of the > parameters "rcoulomb=0.9" I think should b

[gmx-users] GPU CUDA version does not support improper dihedrals?

This surprised me since most of the systems that I am interested in have improper dihedrals. Is it possible that I did something wrong here? ### Error message from mdrun-gpu: Program mdrun-gpu, VERSION 4.0.99-dev-20100315 Source code file: /project/pomes/cneale/GPC/exe/intel/GPUgromacs/gromacs-4

[gmx-users] pdb2gmx-4.5 treats DNA as protein (and fails)

Hi, I'm trying to convert protein-DNA complex using pdb2gmx with gromos53a6.ff $ pdb2gmx -f del.pdb -o del.gro -p del.top -i del.itp -n del.ndx -ignh In gromacs version 4.5-beta2 the result is: Processing chain 3 'C' (516 atoms, 25 residues) There are 0 donors and 0 acceptors There are 0 hydrog

Re: [gmx-users] Conformational sampling

Thanks. I am definitely going to look into that. Quoting chris.ne...@utoronto.ca: Nisha: Simply applying available tools and seeing if the distribution looks okay is not a good plan. You should have a very well-defined idea of what you are trying to test and then pick a tool to get that done.

[gmx-users] pdb atom nomenclature in gmx rtp files

Hi there, I see in ffoplsaa.rtp that, e.g., CYS has: HB1opls_1400.060 2 HB2opls_1400.060 2 But according to latest PDB atom nomenclature it should be: HB2 ... HB3 ... Of course that using pdb2gmx -ignh and it should avoid this problem, but unless for any other spe

Re: [gmx-users] Double Precision Gromacs 4.5 beta 2 on Intel Xeon "Woodcrest"

Hi, This bug is now fixed in git release-4-5-patches (commit 0a31a047f429). Rossen On 8/6/10 11:33 AM, david.groc...@uk.fujitsu.com wrote: Hi, this is the first time I have messaged this group, so please bear with me. I have had little trouble with previous versions (4.0.7 for example), howe

[gmx-users] GMXRC missing

Dear all, I have installed 4.5 beta2 using cmake and it seems that the GMXRC files are missing in the installation. Can anyone confirm this? Best, Ondrej -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www

Re: [gmx-users] Gromacs-4 benchmarking

On 8/10/10 8:40 AM, vivek sharma wrote: Hi There, I want to benchmark the scalability and speed for gromacs-4 on our cluster. I want to know if there is any benchmarking activity already goin on? I have browsed and got benchmarking for gromacs-3 and it seems that gromacs-4 is much more scalab

[gmx-users] Gromacs 4.5-beta2 forcefield troubles

Hi all, I am trying to get 4.5-beta2 running on graphic card but mdrun-gpu (gcc 4.1.3) is still complaining about something in forcefields OPLS - The combination rules of the used force-field do not match the one supported by OpenMM: sigma_ij = (sigma_i + sigma_j)/2, eps_ij = sqrt(eps_i * eps_j)

Re: [gmx-users] Gromacs-4 benchmarking

- Original Message - From: vivek sharma Date: Tuesday, August 10, 2010 16:41 Subject: [gmx-users] Gromacs-4 benchmarking To: Discussion list for GROMACS users > Hi There, > I want to benchmark the scalability and speed for gromacs-4 on our cluster. > I want to know if there is any ben

Re: [gmx-users] Mix two solvents

Use the same box size for both. Then move one box with eidtconf -translate by its boxlength. Afterwards, you can simply put the boxes together to one large one. Quoting tekle...@ualberta.ca: Dear Gromacs, I want to combine two separately equilibrated solvents into one mixed solvent file.

[gmx-users] RE: Large output files and limited disk space. How do I handle them?

Hi guys Thanks for your help! I will consider your suggestions. Huiwen From: NG HUI WEN Sent: Monday, August 09, 2010 11:05 AM To: gmx-users@gromacs.org Subject: Large output files and limited disk space. How do I handle them? Dear gmxusers, I have a very basic question here wh

Re: [gmx-users] Mix two solvents

- Original Message - From: tekle...@ualberta.ca Date: Tuesday, August 10, 2010 13:50 Subject: [gmx-users] Mix two solvents To: gmx-users@gromacs.org > Dear Gromacs, > > I want to combine two separately equilibrated solvents into one > mixed solvent file. How can I do that? I want to c