[gmx-users] Restarting a gromacs calcluation

Mon Mar 19 19:46:57 CET 2007

Dear Tsjerk,

Thank for your help. tbpconv -time works fine.

Ciao,

Luciano

Dr. Luciano Triguero College of Art and Science Department of Physics and Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: 305-284-3938

________________________________

From: gmx-users-bounces at gromacs.org on behalf of Tsjerk Wassenaar
Sent: Sun 3/18/2007 6:31 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Restarting a gromacs calcluation

Hi Luciano,

It may be a good idea to think about the contents of the different
files and the meaning of the messages. If you don't provide a .trr
file, you won't have new coordinates, tpbconv will use those from the
original .tpr and effectively, you will just start the run all over!
Man..., what about tpbconv -h, and following tpbconv with -time to
select a frame for which you have positions, velocities and energies?

Tsjerk

On 3/17/07, Triguero, Luciano O <ltriguero at miami.edu> wrote:
> >> Dear Users,
> >>
> >> Thank for your help. I started a 10 ns simulation, but it dies because of
> >> an error in the cluster PBS system, so I want to continue the simulation
> >> from the last (r,v) point. May I still use tpbconv to restart from that
> >> last point and continue the simulation.
> >>
> Check where your trr or edr file ends using gmxcheck -f or -e. The
> shorter will be used by tpbconv for your new tpr. Specify tpbconv with
> -f and -e.
>
> Dear,
>
> Thank for your answer. I still have a problem. Do you mean (-f and -e) or (-f or -e)
>
> I checked my trr and edr files and edr files ends first, then I typed:
>
> tpbconv   -s md_input.tpr -f <>.trr -e <>.edr -o md_cont.tpr
>
> and got the following error message:
>
> ++++++++++++++++++++++++++++++++++++++++++++++++++
> Opened md_minim_energy.edr as single precision energy file
> Reading frame   4000 time 4000.000
> Last frame read 4876
> WARNING: Incomplete frame: nr   4877 time 4876.000
> -------------------------------------------------------
> Program tpbconv, VERSION 3.3.1
> Source code file: enxio.c, line: 401
> Fatal error:
> Could not find frame with time 4884.000000 in 'md_minim_energy.edr'
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> However, tpbconv runs without error when I provide only option -e <>.edr. Is it correct to restart
> a calculation with the .tpr file generated with only -e <>.edr option. Will be then possible to concatenate trajectories correctely?
>
> Advices,
>
> Thank for your time,
>
> Luciano
>
>
>
> >
> > Sure - as far as I know. It will generate new .tpr, which you will use for
> > starting the simulation - when it is finished, simply concatenate
> > trajectories, energy files with trjcat and eneconv.
> >
> > Milan
> >
> >
> >> Thank again,
> >>
> >> Luciano
> >>
> >> Dr. Luciano Triguero College of Art and Science Department of Physics and
> >> Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box 249118
> >> Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: 305-284-3938
> >>
> >> ________________________________
> >>
> >> From: gmx-users-bounces at gromacs.org on behalf of Yang Ye
> >> Sent: Fri 3/16/2007 8:49 AM
> >> To: Discussion list for GROMACS users
> >> Subject: Re: [gmx-users] Restarting a gromacs calcluation
> >>
> >>
> >>
> >> Can you be more specific? Continue or start new simulation. Use tpbconv
> >> to extend your simulation.
> >>
> >> On 3/16/2007 9:37 AM, Triguero, Luciano O wrote:
> >>
> >>> Dear users,
> >>>
> >>> How do I restart a gromacs simulation?
> >>>
> >>> Ciao,
> >>>
> >>> Luciano
> >>>
> >>> Dr. Luciano Triguero College of Art and Science Department of Physics and
> >>> Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box
> >>> 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office:
> >>> 305-284-3938 _______________________________________________
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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