[gmx-users] several basic questions on GROMACS

[Justin Lemkul]

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

-- 
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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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