[gmx-users] Temperature output file
Vitaly V. Chaban
vvchaban at gmail.com
Fri Oct 23 20:30:22 CEST 2015
Temperature groups have to be defined in the parameter file to derive the
coveted data, I believe.
On Thu, Oct 22, 2015 at 11:05 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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.
>> 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 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
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