[gmx-users] Temperature output file

[Justin Lemkul]

On 10/22/15 9:01 AM, Ali Mohyeddin wrote:
> Dear all,
>
> I am very beginner to gromacs. I have already simulated a simple protein
> using a nice gromacs tutorial.
> (
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html
> )
> Now I want to run some analysis to get the temperatures of protein and
> solvent separately. I have entered the following command but nothing
> written in temperature.xvg file:
>
> gmx traj  -f  md_0_1.xtc  -s  md_0_1.tpr  -ot  temperature.xvg
>
> May anyone help me?
>

There are no velocities in an .xtc file, so temperature can't be calculated. 
Moreover, you have to correct for the influence of constraints.

Simply put, you're using the wrong program for something simple like this.  What 
you want is gmx energy, as all temperature data are stored in the .edr file.

-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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