[Bulk] [gmx-users] tpbconv to continue a run that has

[Cesar Araujo]

Message: 2
Date: Thu, 24 Nov 2005 14:09:41 +0800
From: Yang Ye <leafyoung81-group at yahoo.com>
Subject: Re: [Bulk] [gmx-users] tpbconv to continue a run that has
        finishes
To: wurl04 at iccas.ac.cn,        Discussion list for GROMACS users
        <gmx-users at gromacs.org>
Message-ID: <43855925.4050907 at yahoo.com>
Content-Type: text/plain; charset=GB2312

Hi,

I have the same problem and the reason was that I forgot to save velocities in
trajectory file in addition to coordinates data. If you are not recording
velocities (option nstvout not equal 0 in mdp file) tpbconv cannot determine
how to continue with your simulation, then it restarts from scratch. As a
reference, for a 6ns simulation I was using a value of 25000 for both nstxout
and nstvout. Maybe you want also to record force (nstfout option) that let you
obtain more information on data analysis.

So in conclusion, you will have to restart the simulation from scratch and do
not forget to add the nstxout/nstvout/nstfout options in mdp files.

Regards,
César.-

Rongliang Wu wrote:

>         
> Hello gmx-users,
> ¡¡¡¡i finished an MD run and i found it still unequalized, i used
> tpbconv function to extend my run but it re-ran from scratch. i set
> the "-time" option but it didn't work. i'm sure my tpr and trr input
> has no problem.
> Thanks!
> Best wishes!
> Sincerely,
> Rongliang Wu
> State Key Laboratory
> of Polymer Physics and Chemistry
> Center of Molecular Science
> Institute of Chemistry
> Chinese Academy of Sciences
> wurl04 at iccas.ac.cn <mailto:wurl04 at iccas.ac.cn>
> 2005-11-24

-- 
Cesar Araujo, Lic. of Chemistry
Department of Molecular Endocrynology
Oulu University Hospital
FIN-90029 OYS, FINLAND

phone: +358 8 3155632
e-mail: cesar.araujo at oulu.fi