[gmx-users] several basic questions on GROMACS

[Brett]

Dear Justin,

Suppose at the end of NVT equilibation and before the start of the following NPT equilibation, I intentionally (or by accident) delete the nvt_prev.cpt file from the directory, does it affect the run of the  NPT equilibation step?

Brett









At 2016-04-05 21:27:41, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>On 4/5/16 9:24 AM, Brett wrote:
>> Dear All,
>>
>> Based on the on-line Lysozyme tutorial, I started a MD from energy
>> minimization to NVT equlibation to NPT equlibration, and I am now in the
>> production MD step.
>>
>> When I checked my Directory containing all the MD files for the whole MD
>> process, I find there is a "mdout.mdp". Is my understanding correct on that,
>> in the energy minimization step, it will create a "mdout.mdp" file, and in
>> any of the following of NVT equlibation, NPT equlibration and production MD
>> step, a "mdout.mdp" file will be created and automatically replaced the
>> "mdout.mdp" file created in the previous step?
>>
>
>GROMACS backs up files, it doesn't replace them unless you set GMX_MAXBACKUP=-1.
>
>> As I mentioned, currently I was in the production M step, and if I
>> intentionally delete the "mdout.mdp" file from the Directory, how does it
>> affect my production MD?
>>
>
>mdout.mdp is just to record your options for posterity.  Deleting it has no 
>effect on anything.
>
>> The next question, during my production MD step, I checked my Directory, and
>> here let me take the NVT related files as example, I found there were a
>> nvt.cpt and a nvt_prev.cpt file. Suppose my NVT equilibration step lasts for
>> 100 ps, is the nvt.cpt the file created by "gmx grompp -f npt.mdp -c nvt.gro
>> -t nvt.cpt -p topol.top -o npt.tpr", and the nvt_prev.cpt the cpt file
>> created at the end of "gmx mdrun -deffnm npt -v &", and this nvt_prev.cpt
>> file will be used at the beginning of the next step NPT equilibration?
>>
>
>Look at the time stamps.  Checkpoint files are mdrun output and are written per 
>the mdrun command line -cpt option, which defaults to once every 15 minutes.  A 
>previous checkpoint (*_prev.cpt) is written as a failsafe, in case something 
>goes wrong writing the current checkpoint so you don't lose all your work in the 
>event of a disruption.
>
>-Justin
>
>-- 
>==================================================
>
>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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