[gmx-users] High temperature Simulation

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 17 17:03:59 CEST 2011

Kavyashree M wrote:
> Hello,
>     The set pressure should reflect whatever system you are trying to model.
> This statement is not very clear to me.. But when the mdout.mdp file 
> after grompp
> during energy minimization is examined it says -
> gen-vel                  = no
> gen-temp                 = 300
> gen-seed                 = 173529
> Even though I have not assigned any velocities in em.mdp file. Thats the
> reason why got this doubt about temperature during energy minimization.

I don't see the connection to my comment about pressure, but I'll address this 
anyway.  There is no temperature during EM.  Hence with "gen-vel = no" then no 
velocities are generated.  The settings for gen-temp and gen-seed are defaults 
that are assigned when none are provided in the input .mdp file.

I seem to recall that a pressure term is written during EM, but it is largely 



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


More information about the gromacs.org_gmx-users mailing list