[gmx-users] Extending simulation

[RAHUL SURESH]

Thank you
On Fri, 7 Apr 2017 at 5:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/7/17 5:07 AM, João Henriques wrote:
> > Dear Rahul,
> >
> > I've never worked with gmx-2016, but the error message is extremely
> clear.
> > Therefore I will skip the explanation and just give you the solution.
> > Rename the old tpr as md_old.tpr (or something or the sort) and the new
> > extended one as md.tpr. Then it shouldn't complain because all run files
> > have the same name (md.*) and appending will raise no problems.
> >
>
> Alternatively, do not try to append when changing file names (mdrun
> -noappend)
> and avoid having to rename your files at all.
>
> -Justin
>
> > Best regards,
> > /J
> >
> > On Fri, Apr 7, 2017 at 10:54 AM, RAHUL SURESH <drrahulsuresh at gmail.com>
> > wrote:
> >
> >> I want to extend my simulation for another 15ns. Previously generated
> files
> >> are md.log, md.xtc, md.edr and md.tpr.
> >>
> >> I used the following commands
> >>
> >>
> >>
> >> *gmx convert-tpr -s md.tpr -extend 15000 -o 25nsmd.tpr*
> >>
> >>
> >> *gmx mdrun -s 25nsmd.tpr -cpi md.cpt*
> >> I get the following error
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> *Fatal error:File appending requested, but 2 of the 3 output files are
> not
> >> present or arenamed differently. For safety reasons, GROMACS-2016 and
> later
> >> only allows fileappending to be used when all files have the same names
> as
> >> they had in theoriginal run. Checkpointing is merely intended for plain
> >> continuation of runs.For safety reasons you must specify all file names
> >> (e.g. with -deffnm), andall these files must match the names used in the
> >> run prior to checkpointingsince we will append to them by default. If
> the
> >> files are not available, youcan add the -noappend flag to mdrun and
> write
> >> separate new parts. For mereconcatenation of files, you should use the
> gmx
> >> trjcat tool instead.*
> >> The 2 file missing are
> >> md.edr
> >> md.xtc
> >>
> >> Here I haven't changed any file name then why do i get this error?
> >> --
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> >>
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> >>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*