[gmx-users] Extending simulation

[Justin Lemkul]

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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-- 
==================================================

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

==================================================