[gmx-users] turn off pdb output

[David Mobley]

Erik,

Thanks. That does it. I assume you guys will put something like this into CVS?

Thanks again -- this is a lifesaver. I've had a couple hundred of
these trajectories to reprocess and haven't been able to do it without
filling my disk with unwanted pdb files.

David

On 3/23/07, Erik Lindahl <lindahl at cbr.su.se> wrote:
> Hi,
>
> Ah, then it's probably because of the rerun. I bet we're never making
> a call to low_constrain with bInit set, which means the variable
> isn't set.
>
> Try this:
>
>   Edit low_constrain() in constr.c so to make bDumpOnError an integer
> instead of boolean, and initialize it to -1.
>
> Then cell getenv() (which can be slow) outside the init part, but
> only if bDumpOnError==-1, and set it to 0 or 1. Finally edit the
> conditionals for bDumpOnError to check if it is 1 instead.
>
> Cheers,
>
> Erik
>
>
>
> On Mar 22, 2007, at 5:30 PM, David Mobley wrote:
>
> > Erik, Berk,
> >
> >> Hi David,
> >>
> >> It doesn't matter - we just check if it is set at all, i.e. whether
> >> getenv("NO_SHAKE_ERROR") returns NULL or not.
> >
> > I still get PDB files written out due to shake errors using mdrun
> > -rerun in 3.3 when running after doing "setenv NO_SHAKE_ERROR".
> >
> > David
> >
> >>
> >> Cheers,
> >>
> >> Erik
> >>
> >>
> >> On Mar 22, 2007, at 12:59 AM, David Mobley wrote:
> >>
> >> > Berk,
> >> >
> >> > What value does this need to be set to for it to work?
> >> >
> >> > Thanks,
> >> > David
> >> >
> >> >
> >> > On 3/20/07, Berk Hess <gmx3 at hotmail.com> wrote:
> >> >>
> >> >> There seems to be an environment variable NO_SHAKE_ERROR
> >> >>
> >> >> Berk.
> >> >>
> >> >>
> >> >> >From: "David Mobley" <dmobley at gmail.com>
> >> >> >Reply-To: Discussion list for GROMACS users <gmx-
> >> users at gromacs.org>
> >> >> >To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> >> >> >Subject: [gmx-users] turn off pdb output
> >> >> >Date: Mon, 19 Mar 2007 10:28:42 -0700
> >> >> >
> >> >> >All,
> >> >> >
> >> >> >Under some circumstances, mdrun writes out pdb files with
> >> >> previous and
> >> >> >current coordinates. Is there some way I can turn this off?
> >> >> >
> >> >> >For reasons I'd rather not explain, I'm reprocessing a single
> >> >> >precision trajectory using the double precision version of mdrun,
> >> >> and
> >> >> >this results in pdb files being written every step. For obvious
> >> >> >reasons, I would like to avoid this.
> >> >> >
> >> >> >Thanks,
> >> >> >David
> >> >> >_______________________________________________
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