[gmx-users] how to assign options of the same type?

[Justin Lemkul]

On 5/24/15 8:29 AM, Zhang, Cheng wrote:
> Dear GROMACS,
>
> Can I ask how to assign options of the same type?
>
>
> For example, on the website of
>
> http://manual.gromacs.org/current/programs/gmx-mdrun.html
>
>
> It is said in the "Synopsis":
>
>
> [-o [<.trr/.cpt/...>]
>
>
> I want to name the output files as md.trr and md.cpt. However, the followings do not work:
>
>
> -o md.trr md.cpt
>
> -o md.trr/md.cpt
>
> -o md.trr -o md.cpt
>
>
> So do you know what is the syntax?
>

You can't specify multiple files to any option that is not labeled "Mult."  In 
the case of mdrun -o, that is the output trajectory format.  The general help 
info in the synopsis indicates that this file type may be interchangeable in a 
general sense, but here it is somewhat misleading.  You shouldn't try to output 
a checkpoint file in lieu of your trajectory.  The .cpt is produced 
(automatically) with -cpo.

-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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