[gmx-users] Re: Re: rerun of trajectory how to deal with the huge .trr file?

[Nuno R. L. Ferreira]

----- Original Message ----- 
From: "Dallas Warren" <dallas.warren at vcp.monash.edu.au>
To: <gmx-users at gromacs.org>
Sent: Monday, March 08, 2004 10:28 PM
Subject: Re: [gmx-users] Re: Re: rerun of trajectory how to deal with the
huge .trr file?


>
> >1/ when runing mdrun,how can i keep water molecule out of the output
> >file(such as.trr)   in order to minmize the size of the outpur file
>
> You can't during the run with .trr files (I don't think you can, haven't
> seen anything that indicates you can).  Afterwards, you can use trjconv to
> remove the water, but not while the simulation is running etc.
>

But you can choose which groups to write to your xtc trajectory.
Use for eg:

dt = 0.002
xtc_grps protein
nstxtcout 500

and you will write to a xtc file every ps only the coords of your protein.

As Dr. Warren said, I also don't think that this can be done to a trr file.
But it will be fine thought to have a flag for this.

Kind regards,
Nuno


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Nuno Ricardo Santos Loureiro da Silva Ferreira
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra - Portugal
Fax: +351 239 827703  - www.biolchem.qui.uc.pt
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