[gmx-developers] how to extend a run using tpbconv?

[spitaleri.andrea at hsr.it]

Hi Berk,
thanks for your reply. I followed your suggestion but I did not work.
Basically:
1. tpbconv -s old -extend (or until) -o new -> it does not work (it ask
for trr)

2. tpbconv -s old -nsteps -o new 
2a. mdrun -s new -cpi file.cpt 
it crashes with this error:

Program mdrun, VERSION 4.0_beta1
Source code file: domdec.c, line: 5627

Fatal error:
The size of the domain decomposition grid (12) does not match the number
of nodes (24). The total number of nodes is
 24

The only way to get to work it is in the old fashion:
tpbconv -s -extend -o new -f -e
mdrun -s new (without file.cpt)

I am just wondering wheter the last procedure is still correct.

Thanks in advance

andrea

Andrea Spitaleri PhD
Dulbecco Telethon Institute 
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153

----- Original Message -----
From: Berk Hess <hessb at mpip-mainz.mpg.de>
Date: Tuesday, September 16, 2008 5:00 pm
Subject: Re: [gmx-developers] how to extend a run using tpbconv?

> Hi,
> 
> Extending is only required if you want more steps then you 
> initially set 
> in your mdp file.
> 
> The procedure is to first modify only nsteps in your tpr file and 
> then 
> continue from the checkpoint file:
> 1 tpbconv -s old -extend (or -until or -nsteps) -o new
> 2 mdrun -s new -cpi file.cpt
> 
> Berk
> 
> andrea spitaleri wrote:
> > Hi then,
> > I see that now gromacs can read checkpoint file. Which is now 
> the 
> > right procedure to extend a simulation using tpbconv?
> >
> > 1. tpbconv -s file.tpr -f file.cpt -extend 1000 -o new
> > or
> > 1. tpbconv -s file.tpr -f file.trr -extend 1000 -o new
> >
> > 2. mdrun -s new
> > or
> > 2. mdrun -s new -cpi file.cpt
> >
> > Then, do I need to keep the same number of cpus of the previous 
> run or 
> > I can change?
> >
> > thanks in advance
> >
> > Regards,
> >
> > andrea
> >
> 
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