[gmx-users] Re: NPT simulation for mutation study (Justin A. Lemkul)

Shyno Mathew sm3334 at columbia.edu
Mon Apr 16 19:15:31 CEST 2012

Hey Justin,

thanks for your reply.
For gen_vel, the manual says "Generate velocities in grompp according to a
Maxwell distribution at temperature gen_temp [K], with random seed
gen_seed. This is only meaningful with integrator
Since the integrator I am using is sd, I put 'gen_vel no'
Yes you are correct, this is equilibration.
>From what you are saying, even with sd as the integrator, I guess, I should
gen_vel       yes
gen_temp   310  ; i want to do the simulation at 310K


Shyno Mathew
PhD student
Department of Chemical Engineering
Columbia University
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120416/885830be/attachment.html>

More information about the gromacs.org_gmx-users mailing list