[gmx-users] trr file

[Dan Gil]

Hi Rita,

How long did your simulation run? If it happens to be very long and you do
not want to run the simulation again, perhaps you can try analyzing it in
pieces.

Use trjconv with -b and -e options to extract small pieces of the .trr file
at a time. Analyze the small pieces, delete the .xtc file, and use trjconv
again to get the next piece from .trr.

Dan

On Sat, Oct 15, 2016 at 6:43 AM, Diana Lousa <dlousa at itqb.unl.pt> wrote:

> Hi Rita,
>
> If none of this works, you can try a to do a rerun (run mdrun with the flag
> -rerun). You can provide a new mdp where you can tell gromacs to write an
> xtc with the frequency output that you want (using a lower frequency will
> generate a smaller xtc file)
>
> Good work!
>
> On Sat, Oct 15, 2016 at 6:37 AM, tasneem kausar <tasneemkausar12 at gmail.com
> >
> wrote:
>
> > Hi
> > I think you can try analysis in more than one step by using -b and -e
> > option of trjconv.
> >
> > On Fri, Oct 14, 2016 at 5:59 PM, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > Prevention is the best medicine - ask google about reducing GROMACS
> > > trajectory storage volume :-)
> > >
> > > Mark
> > >
> > > On Fri, Oct 14, 2016 at 1:20 PM Nuno Azoia <nazoia at gmail.com> wrote:
> > >
> > > > Have you tried the option -split?
> > > > I never tried, and I don't know if it will solve your problem, but
> give
> > > it
> > > > a try.
> > > >
> > > >
> > > > On Fri, Oct 14, 2016 at 11:34 AM, Rita Paiva Melo <
> > > > ritamelo at ctn.tecnico.ulisboa.pt> wrote:
> > > >
> > > > > Hello,
> > > > >
> > > > > Thank you for your suggestions. I have already tried run trjconv
> but,
> > > as
> > > > > trajectory is heavy and server is full, out of memory error appears
> > and
> > > > > analysis tool crash.
> > > > >
> > > > > Best,
> > > > > Rita.
> > > > >
> > > > > -----Original Message-----
> > > > > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
> > > > > gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of
> Nuno
> > > > Azoia
> > > > > Sent: 14 de outubro de 2016 11:19
> > > > > To: gmx-users at gromacs.org
> > > > > Subject: Re: [gmx-users] trr file
> > > > >
> > > > > Hello Rita,
> > > > >
> > > > > I think the answer is trjconv. Try to convert it to xtc, reduce the
> > > > number
> > > > > of frames (with dt or skip), or reduce the components on the
> > > trajectory.
> > > > If
> > > > > you don't need solvent for the calculations you can create a
> > trajectory
> > > > > without it. Removing the solvent and convert it to xtc should have
> a
> > > > great
> > > > > impact in file size.
> > > > >
> > > > > Nuno Azoia
> > > > >
> > > > > On Fri, Oct 14, 2016 at 11:04 AM, Rita Paiva Melo <
> > > > > ritamelo at ctn.tecnico.ulisboa.pt> wrote:
> > > > >
> > > > > > Dear all,
> > > > > >
> > > > > > Probably a rookie question but anyone knows how to reduce
> > trajectory
> > > > > > volume file to be analyzed (I have already tried trjconv)? I
> have a
> > > > > > trr file with  167 GB and analysis tools crash.
> > > > > >
> > > > > > Thanks,
> > > > > > Rita.
> > > > > >
> > > > > > --
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> --
> Diana Lousa
> Post-doc
> Protein Modeling Laboratory
> ITQB/UNL
> Oeiras, Portugal
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