[gmx-users] Problem with temperature and stochastic dynamics in FEP

Sanku M msanku65 at yahoo.com
Wed Aug 3 21:06:30 CEST 2011

Yes. I did check the tau_t issue. I used tau_t=2ps as recommended in the manual.
Again here, the simulation with 0.002 ps step gives rise to 303K. But, from now 
on, as per your( and Justin's) recommendation, I am going to use the tau_t=2ps 
and rvdw<rlist in conjunction with 0.001 ps time step when using sd integrator 
from my production/equilibration run for all lambda.

From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wed, August 3, 2011 11:00:30 AM
Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

 On 4/08/2011 1:51 AM, Sanku M wrote: 
Hi Mark and Justin,
>  I did investigate on the rvdw=rlist issue. But, I found           even if I 
>make rvdw < rlist and still keep time step 0.002,           the average 
>temperature goes to 303 K.
>Only reducing the time step does help ( even if rvdw=rlist)           to get 
>average temperature to 300K.
... and the tau_t issue I mentioned?

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110803/9cb029b4/attachment.html>

More information about the gromacs.org_gmx-users mailing list