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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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