[gmx-users] Restarting a gromacs calcluation

[Tsjerk Wassenaar]

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