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