[gmx-users] High Initial generated Temp

Justin Lemkul jalemkul at vt.edu
Tue Jun 4 14:16:53 CEST 2013

On 6/4/13 8:07 AM, tarak karmakar wrote:
> Dear All,
> Although I have set gen_temp = 300, it is showing the initial temperature
> 445.7 K, generated at the very beginning  of the run.
> gen_vel                 = yes             ; velocity generation
> gen_temp                = 300
> gen_seed                = 93873959697
> Is it because of a bad geometry? In mailing list I came across this thread
> [ http://comments.gmane.org/gmane.science.biology.gromacs.user/41931]
> Prior to this production run, I heated my system slowly from 0 K to 300 K
> within 300 ps time span.
> It would be very helpful if someone suggests me the way to deal with this
> problem?

A full .mdp file is always more useful than a small snippet.  I have seen this 
same behavior when the "continuation" parameter is incorrectly set - have you 
used "continuation = yes" in your .mdp file?  If not, the constraints get messed 
up and your initial velocities can get all messed up.

A larger point is this - why are you re-generating velocities after heating the 
system from 0 to 300 K?  Why not simply preserve the ensemble at 300 K by using 
a .cpt file?



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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