[gmx-users] Syntax to use "gmx convert-tpr"

[Justin Lemkul]

On 6/8/15 10:10 AM, Zhang, Cheng wrote:
> Dear GROMACS experts,
>
> Can I ask if the following commandlines are correct for extending simulations?
>
>
> gerun convert-tpr -s md_0_1.tpr -f md_0_1.trr -e md_0_1.edr -o md_0_1.tpr
>

The command is "gmx convert-tpr" and it is not parallelized.  You do not need 
.trr or .edr files, and here you haven't actually provided it any instructions 
to do anything useful.  Start by reading the help info and doing some tutorials.

> gerun mdrun_mpi -deffnm md_0_1 -cpi md_0_1.cpt -maxh 0.5 -append
>
>
> (My job.sh can be found at https://copy.com/lrFubrlq9fos04Zy)
>
>
> My questions are:
>
>
> 1) For the 1st job, there are no .trr and .edr files. So the "convert-tpr" will be ignored?
>

No, this command will simply fail.  The first .tpr file is created by grompp, 
and subsequently amended with convert-tpr.  Again, simple tutorials cover this.

>
> 2) Should I use "-f md_0_1.trr" or "-f md_0_1.cpt" as shown on
>
> http://manual.gromacs.org/programs/gmxconverttpr.html   ?
>

Providing .trr and .edr files is the ancient (e.g. version < 4.0) method of 
using the program, so no.

>
> 3) What is "index.ndx" file used for? I cannot find them as outputs of a simulation. Do I need to include that?
>

This is not relevant here.  The convert-tpr program can create subset .tpr files 
that can be useful for analysis.  You don't need one.

-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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