[gmx-users] trr file

[Diana Lousa]

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