[gmx-users] Problem with temperature and stochastic dynamics in FEP
Sanku M
msanku65 at yahoo.com
Wed Aug 3 04:42:32 CEST 2011
OKK, But, before, I have tried using md as integrator where I start the initial
velocity as 280K ( which makes sense as the minimized configuration is
essentially at low temperature) and have used Nose-hoover at 300K and I never
had problem in getting the desired 300K after running a short NVT simulation as
equilabration.
The problem arises when sd integrator is used.
In fact, I just tried to generate the initial velocity at 300K along with sd
integrator. I got the 303 K as average temperature again. The same simulation
using md integrator always gives rise to 300K as average temperature( when used
in conjunction with Nose-Hoover ) , even if I generate velocity at 280 K or 300K
.
I guess that the initial velocity-generation temperature should not be an issue
here. The sd integrator in contrast to md integrator may be the problem.
________________________________
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tue, August 2, 2011 8:40:21 PM
Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP
Sanku M wrote:
> Hi Justin,
> So, do you suggest that after minimization, I should generate the velocity at
>300K instead ?
> i.,e for equilibration,should following the set-up?
>
You should always equilibrate under the desired conditions. Never make sudden
changes, or else you're going to damage the stability of the system.
-Justin
> gen-vel = yes
>> > gen-temp = 300
>> > gen-seed = -1
>
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Tue, August 2, 2011 8:26:16 PM
> *Subject:* Re: [gmx-users] Problem with temperature and stochastic dynamics in
>FEP
>
>
>
> Justin A. Lemkul wrote:
> >
> >
> > Sanku M wrote:
> >> Hi Justin,
> >> I first performed two minimization using steep and l-bfgs as the method on
>the solvated system for each lambda. Then I ran a 500ps NVT simulation on
>minimized system ( for each lambda) where essentially same .mdp file was used
>except the following change:
> >> gen-vel = yes
> >> gen-temp = 280
> >> gen-seed = -1
> >>
> >> So, essentially, I heated the minimized system up from 280 K with ref_t
>300K using sd integrator. But, here also I found the average temperature goes to
>303 K( instead of 300 K) .
> >
> > Unless you did simulated annealing in between, you didn't heat the system,
>you suddenly jolted the temperature, which is probably not stable. Maybe the
>integrator/Langevin thermostat does not react well to these conditions.
>Equilibrate under the conditions you wish to collect data. Your data collection
>uses NPT, so running NVT at a different temperature and suddenly changing the
>temperature and introducing pressure coupling is not an appropriate procedure.
>If nothing else, your data will be unreliable, even if your temperature was
>correct.
> >
>
> Sorry, misread the previous .mdp settings. You're still using NVT, but the
>point about the temperature is still valid here.
>
> -Justin
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> -- gmx-users mailing list gmx-users at gromacs.org
><mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
>http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface or
>send it to gmx-users-request at gromacs.org <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
-- gmx-users mailing list gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or
send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> -- gmx-users mailing list gmx-users at gromacs.org
><mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
>http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface or
>send it to gmx-users-request at gromacs.org <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
-- gmx-users mailing list gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or
send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> -- gmx-users mailing list gmx-users at gromacs.org
><mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
>http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface or
>send it to gmx-users-request at gromacs.org <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
-- gmx-users mailing list gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or
send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> -- gmx-users mailing list gmx-users at gromacs.org
><mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
>http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface or
>send it to gmx-users-request at gromacs.org <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
-- gmx-users mailing list gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or
send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110802/07ac00ed/attachment.html>
More information about the gromacs.org_gmx-users
mailing list