huifang liu wrote:
Hello, everybody,
I recently installed FFTW-3.0.1, mpich-1.2.7 and Gromacs 3.3.3 on my
workstation with two 8-cords CPUs. I think i installed them correctly,
beause it runs normally with other parellel MD software. It also went
nomorally when i run mdrun command in groma
Hello, everybody,
I recently installed FFTW-3.0.1, mpich-1.2.7 and Gromacs 3.3.3 on my
workstation with two 8-cords CPUs. I think i installed them correctly,
beause it runs normally with other parellel MD software. It also went
nomorally when i run mdrun command in gromacs with 4 nodes. The prob
0.tpr.
-Original Message-
From: "Berk Hess" <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Date: Fri, 23 Nov 2007 10:58:48 +0100
Subject: Re: RE: [gmx-users] problem with mdrun performing replica exchange
MD
You need to supply the -np option.
In Gromacs 3.3 you don'
argument.
Berk.
From: "OZGE ENGIN" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: gmx-users@gromacs.org
Subject: Re: RE: [gmx-users] problem with mdrun performing replica exchange
MD
Date: Fri, 23 Nov 2007 11:44:47 +0200
Hi Berk,
I indicated the numbe
original hint was also confusing.
I meant that you should use mpirun with the -np option.
Berk.
From: "OZGE ENGIN" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: gmx-users@gromacs.org
CC: gmx-users@gromacs.org
Subject: Re: Re: RE: [gmx-users] problem with
ssage-
From: "Berk Hess" <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Date: Fri, 23 Nov 2007 10:58:48 +0100
Subject: Re: RE: [gmx-users] problem with mdrun performing replica exchange MD
You need to supply the -np option.
In Gromacs 3.3 you don't need to set the -multi
have such a file: simul00.tpr
-Original Message-
From: "Berk Hess" <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Date: Fri, 23 Nov 2007 10:58:48 +0100
Subject: Re: RE: [gmx-users] problem with mdrun performing replica exchange MD
You need to supply the -np option.
In Gro
OTECTED]>
To: gmx-users@gromacs.org
Date: Fri, 23 Nov 2007 10:58:48 +0100
Subject: Re: RE: [gmx-users] problem with mdrun performing replica exchange MD
You need to supply the -np option.
In Gromacs 3.3 you don't need to set the -multi option,
and -multi does not take an argument.
If you us
: Discussion list for GROMACS users
To: gmx-users@gromacs.org
Subject: Re: RE: [gmx-users] problem with mdrun performing replica exchange
MD
Date: Fri, 23 Nov 2007 11:44:47 +0200
Hi Berk,
I indicated the number of replicas with -multi option. In additon, I have
compiled Gromacs with MPI support.
t;
To: gmx-users@gromacs.org
Date: Fri, 23 Nov 2007 10:36:57 +0100
Subject: RE: [gmx-users] problem with mdrun performing replica exchange MD
>From: "OZGE ENGIN" <[EMAIL PROTECTED]>
>Reply-To: Discussion list for GROMACS users
>To: gmx-users@gromacs.org
>Subject: [gmx-
From: "OZGE ENGIN" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: gmx-users@gromacs.org
Subject: [gmx-users] problem with mdrun performing replica exchange MD
Date: Fri, 23 Nov 2007 11:30:53 +0200
Hi All,
I am performing replica exchange molecular dyn
Hi All,
I am performing replica exchange molecular dynamics simulation(REMD). I have 16
replicas each of which has a peptide with different conformation. After
obtaining .tpr files (at desired temperatures) for each replicas, I loaded them
via mdrun, but I got the following error:
Fatal error:
> tcoupl = Berendsen
> tc-grps = Protein SOL DRG Cl
> tau_t = 0.1 0.1 0.1 0.1
> ref_t = 300 300 300 0.1
This could also be a problem. Never couple solvent and ions separately. Also
note that you have your temperature of Cl
Blaise Mathias-Costa wrote:
Hello All,
The program was stopped twice with the following error:
Constraint error in algorithm Lincs at step 54646
t = 109.292 ps: Water molecule starting at atom 13293 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with
Hello All,The program was stopped twice with the following error: Constraint error in algorithm Lincs at step 54646t = 109.292 ps: Water molecule starting at atom 13293 can not be settled.Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinatesGrid:
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