[gmx-users] Addendum to Question

[Justin Lemkul]

On 3/12/16 11:51 AM, Robert Molt wrote:
> Thank you for clarifying the proper way to search the forums.
>
> I was perhaps unclear in what I wrote. I already *have *the converted topology
> and trajectory files (via Parmed). Rather, I am seeking the correct command to
> combine them into a binary (pursuant to the use of do_x3dna
> http://rjdkmr.github.io/do_x3dna/usage.html; this states I need to use a binary).
>
> Am I incorrect in thinking I need to apply some form of the gmx command to a gro
> trajectory file and a topology file to make a tpr file (which is a binary and
> thus not directly convertible from what I have)?
>

You need to use grompp.  It creates a .tpr by combining coordinates (not 
trajectory!), topology, and simulation instructions (which in this case are 
arbitrary, as you only care to do analysis) into a binary input file with a .tpr 
extension.

-Justin

> I will begin examining your tutorials, Dr. Lemkul. Thank you.
>

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

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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