[gmx-users] Extending simulation
jalemkul at vt.edu
Fri Apr 7 14:02:26 CEST 2017
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.
> Best regards,
> On Fri, Apr 7, 2017 at 10:54 AM, RAHUL SURESH <drrahulsuresh at gmail.com>
>> 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
>> Here I haven't changed any file name then why do i get this error?
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
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