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

Lee Soin wrote: Does GROMACS have a multi-thread implementation, instead of using MPI? No, at least not yet. Carsten ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at htt

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

Does GROMACS have a multi-thread implementation, instead of using MPI? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please

[gmx-users] Retrieving .trr file?

Thank you very much Tsjerk. Hi Minnale, >You could've checked the archives. Searching on "trr" and "deleted" >would have yielded (among others): >http://www.gromacs.org/pipermail/gmx-users/2008-May/034217.html > >Tsjerk On Tue, Jun 24, 2008 at 5:40 AM, minnale wrote: > > Hi gmx users, >

Re: [gmx-users] Retrieving .trr file?

Hi Minnale, You could've checked the archives. Searching on "trr" and "deleted" would have yielded (among others): http://www.gromacs.org/pipermail/gmx-users/2008-May/034217.html Tsjerk On Tue, Jun 24, 2008 at 5:40 AM, minnale <[EMAIL PROTECTED]> wrote: > > Hi gmx users, > I have deleted

[gmx-users] Retrieving .trr file?

Hi gmx users, I have deleted *.trr file by mistake, Can anyone tell is there anyway to retrive *.trr file, remaining all *.tpr *.edr *.gro *.log files there. Thanks in advance.___ gmx-users mailing listgmx-users@gromacs.org http://www.groma

Re: [gmx-users] Newbie question

Hi, Of course I can't add anything to the comments regarding the solvent and ions ;) The #include "ions.itp" is commonly added through pdb2gmx in the >3.1 versions, so it shouldn't be necessary to add that (and it isn't for the tutorial (v3.3.3). Anyway, it's good to keep in mind though that the i

[gmx-users] RE: mdp files

> Thanks for the tutorial. I was going through the steps and ran into a > problem when placing in the ions in order to neutralize the system. Would > this because my version of Gromacs is 3.1 and your tutorial is for v3.3.3? I suppose you can add these ions even by hand. It shouldn't be a very big

Re: [gmx-users] MPICH2 and parallel Gromacs errors

Hello, here our scripts for running mdrun with mpich2: mpdboot.sh : #!/bin/sh NODES=7 HFILE=./mpd.hosts # -- MPI=/opt/MPICH2/bin $MPI/mpdboot -v -n `expr $NODES + 1` -f $HFILE -r /usr/bin/rsh -m $MPI/mpd eof mpd.hosts: node1 node2 node3 node4 node5 n

Re: [gmx-users] Re: The number of PME nodes

Carsten Kutzner wrote: Hi Xuji, xuji wrote: Hi Carsten: First, thanks for your reply. Second, someone in the mailing-list said:"Please cut of your email from the digest. It confuses people." And it seems that there's no other people that is interest in this topic. So I

Re: [gmx-users] Re: The number of PME nodes

Carsten Kutzner wrote: > Hi Xuji, > > xuji wrote: > >> Hi Carsten: >> >> First, thanks for your reply. >> Second, someone in the mailing-list said:"Please cut of your email >> from the digest. It confuses people." And it seems that there's no other >> people that is interest in this

Re: [gmx-users] Newbie question

Hi Andres, in total you have 10475 (198+10277) SOL molecules, so you can condense the two SOL lines into one. Suppose you add 20 NA+ and 20 CL-, you subtract 40 SOL molecules from the system and add 40 ions in total. So you write: [ molecules ] ; Compound#mols Protein_A 1 SOL

Re: [gmx-users] Newbie question

Andres Rojas Guerrero wrote: Hi, I'm newbie in Gromacs and MD, I'm reading the Tsjerk excellent tutorial. In the part of Addition of Ions, Tsjerk said that we need to edit the topology file and the decrease the number of solvent molecules, and add a line specifying the number Na+ and Cl-. How

[gmx-users] Newbie question

Hi, I'm newbie in Gromacs and MD, I'm reading the Tsjerk excellent tutorial. In the part of Addition of Ions, Tsjerk said that we need to edit the topology file and the decrease the number of solvent molecules, and add a line specifying the number Na+ and Cl-. How can I do this? Let me exp

Re: [gmx-users] Re: The number of PME nodes

Carsten Kutzner wrote: > Hi Xuji, > > xuji wrote: >> Hi Carsten: >> >> First, thanks for your reply. >> Second, someone in the mailing-list said:"Please cut of your email >> from the digest. It confuses people." And it seems that there's no other >> people that is interest in this topi

Re: [gmx-users] RE: mdp files

[EMAIL PROTECTED] wrote: Hi Tsjerk, Thanks for the tutorial. I was going through the steps and ran into a problem when placing in the ions in order to neutralize the system. Would this because my version of Gromacs is 3.1 and your tutorial is for v3.3.3? Quite possibly. There are few good reas

Re: [gmx-users] RE: mdp files

That depends on what the problem is. It's always best to quote the exact error message when asking for help :-) If you're referring to the use of -conc and -neutral, those were not available in version 3.1. It's always recommended to use the newest version of the software, unless, for some s

[gmx-users] Re: The number of PME nodes

Hi Xuji, xuji wrote: > > Hi Carsten: > > First, thanks for your reply. > Second, someone in the mailing-list said:"Please cut of your email > from the digest. It confuses people." And it seems that there's no other > people that is interest in this topic. So I think it's maybe better

Re: [gmx-users] RE: mdp files

Hi Tsjerk, Thanks for the tutorial. I was going through the steps and ran into a problem when placing in the ions in order to neutralize the system. Would this because my version of Gromacs is 3.1 and your tutorial is for v3.3.3? Thanks for the help, -John > Hi, > > For a tutorial and a workflo

Re: Re: [gmx-users] Meaning of CT, C_2, C_3 in ffoplsaabon.itp

Dear Gayen, It stands for different atom types of the same element. For instance, in all atom OPLS parameter model for acetone, following atom types are being used. CT, 0_2, C_2 and HC for methyl carbons, keto oxygen, carbonyl carbon and methyl hydrogens respectively. Indeed, CT( for methyl