[gmx-users] POPC structure

Hi all, I found 128 popc lipid molecules in prof Tieleman's website ,I want to work on lipids with more than 128 popc lipid molecules, I knew that with help of VMD generate popc lipid molecules how many number we want. Can anyone suggest anyother website. Thanks in advance. _

Re: [gmx-users] Does GROMACS have a multi-thread implementation?

But I see that in mdrun there's an option nt--number of threads to start on each node. Does this mean multi-thread? 2008/6/24 Carsten Kutzner <[EMAIL PROTECTED]>: > Lee Soin wrote: > >> Does GROMACS have a multi-thread implementation, instead of using MPI? >> > No, at least not yet. > > Carsten >

[gmx-users] ngmx. molecules or atoms numbers?

What numbers (of molecules or of atoms?) should contain 'index.ndx' in "ngmx -n index.ndx" ? When using 'index.ndx' with molecules numbers it seems to read it as those of atoms and when using 'index.ndx' with atoms it just refuses to start (the section appeared in display->filter is inactive, I

Re: [gmx-users] ngmx. molecules or atoms numbers?

On Tue, 24 Jun 2008 10:26:27 +0300 Vitaly Chaban <[EMAIL PROTECTED]> wrote: What numbers (of molecules or of atoms?) should contain 'index.ndx' in atoms "ngmx -n index.ndx" ? When using 'index.ndx' with molecules numbers it seems to read it as those of atoms and when using 'index.ndx' with

Re: [gmx-users] Does GROMACS have a multi-thread implementation?

Lee Soin wrote: But I see that in mdrun there's an option nt--number of threads to start on each node. Does this mean multi-thread? Yes, nt means number of threads. It's already there for a future version. Carsten ___ gmx-users mailing listgmx-us

Re: [gmx-users] Does GROMACS have a multi-thread implementation?

For latest stable 3.3.3, there is no multi-thread implementation. For CVS version for coming 4.0, might be, I am not sure, but that's only for testing. Your question tricky without indicating the version. Regards, Yang Ye Lee Soin wrote: But I see that in mdrun there's an option nt--number of

Re[2]: [gmx-users] ngmx. molecules or atoms numbers?

Xavier, Thank for a clarification. Don't you have any ideas why 'ngmx' can have display->filter dialog inactive? Except the case when index-file in wrong-formatted? XP> On Tue, 24 Jun 2008 10:26:27 +0300 XP> Vitaly Chaban <[EMAIL PROTECTED]> wrote: >> What numbers (of molecules or of atoms?)

Re: [gmx-users] Does GROMACS have a multi-thread implementation?

Thanks! 2008/6/24 Carsten Kutzner <[EMAIL PROTECTED]>: > Lee Soin wrote: > >> But I see that in mdrun there's an option nt--number of threads to start >> on each node. Does this mean multi-thread? >> > Yes, nt means number of threads. It's already there for a future version. > > > Carsten > > __

Re: Re[2]: [gmx-users] ngmx. molecules or atoms numbers?

On Tue, 24 Jun 2008 11:24:46 +0300 Vitaly Chaban <[EMAIL PROTECTED]> wrote: Xavier, Thank for a clarification. Don't you have any ideas why 'ngmx' can have display->filter dialog inactive? Except the case when index-file in wrong-formatted? No idea! Never used ngmx. Although it seems to be us

Re: [gmx-users] POPC structure

You can use genconf to replicate the 128-lipid system any number of times you wish. You can also generate replicates of a subset of these lipids (say if you wanted to replicate only 100 of them) by identifying which residues you want, using genconf, and equilibrating thoroughly. A similar dis

[gmx-users] less number of 1-4 parameter combination

Hi all, I have built a topology file for chaps in OPLS force field with inserted hydrogen atoms along with bonds, angles, dihedrals etc parameters using the original topology from prodrg2. The problem is now, grompp results as, Generated 342378 of the 342378 non-bonded parameter combinations G

Re: [gmx-users] less number of 1-4 parameter combination

You might find the following thread informative. It regards CHARMM specifically, but Mark's reply to my question was very useful, and is generally applicable: http://www.gromacs.org/pipermail/gmx-users/2008-February/032529.html -Justin ANINDITA GAYEN wrote: Hi all, I have built a topology

Re: [gmx-users] change coloumb interaction

Thank you Mark for your fast and helpful suggestion ! I read the manual concerning the user defined potential (manual 6.6 and 7.3.11) and I have again some question : 1. In the mdp file I chose :energygrps: Protein SOL energygrp

[gmx-users] Re: modifying g_mdmat

Dear gmx-users, A week ago I was asking about outputting the raw pairwise matrices (instead of XPM-formatted output) for minimum distances between residues in a protein using g_mdmat. I finally got around to poking around in the code and it turned out to be dead easy, just a matter of ta

[gmx-users] Planar molecules / virtual sites

Hi All, I try to simulate with gromacs substituted ethlyle series of molecules (planar) and I have to keep molecules rigid. In case of atomic substitutes, I use 3 virtual sites on the plane of molecule, that reproduce mass and moment of inertia, I use 3 constrains to keep them rigid and the mass

[gmx-users] constraints

Dear Gromacs Users, I have a problem in running the energy minimization of a protein along with a substrate. In the .mdp file, if I use constraints = all-bonds, the system complains like the convergence is reached to system accuracy not to the one I mentioned. If I replace the constraints = none,

Re: [gmx-users] constraints

rams rams wrote: Dear Gromacs Users, I have a problem in running the energy minimization of a protein along with a substrate. In the .mdp file, if I use constraints = all-bonds, the system complains like the convergence is reached to system accuracy not to the one I mentioned. I don't unde

Re: [gmx-users] change coloumb interaction

Sang-Min Park wrote: Thank you Mark for your fast and helpful suggestion ! I read the manual concerning the user defined potential (manual 6.6 and 7.3.11) and I have again some question : 1. In the mdp file I chose :energygrps: Protein SOL

[gmx-users] (no subject)

Hello, I am new to GROMACS, and so my questions my seem relatively simple. I'm attempting to use the AFM Pulling facet of the program to generate force extension curves of ~20 amino acid polypeptide chains. After cutting down my .pdb file to the desired amino acids, i used the command: pdb2g

[gmx-users] Terminal specification for DNA in Gro96 ff

Dear All, I am trying to simulate a protein-DNA system using Gromos96 53a6 forcefield. Could anybody tell me how to specify the terminals for DNA? There is no termini database entry for DNA for this forcefield. Thank you, Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical