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

[Sanku M]

    Finally, I achieved the desired 300K average temperature using sd integrator 
. I had to reduce the time step from 0.002 ps to 0.001 ps and then running the 
NVT could produce 300K as average temperature.
Still Not sure why md integrator still could 300K average temperature using 
0.002 ps as time-step.



________________________________
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tue, August 2, 2011 10:16:17 PM
Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP



Sanku M wrote:
> Hi Justin,
>    I did calculate the average temperature using last 2 ns of the 8ns data. It 
>is still same 303K. 
>
> 

Going back to the original .mdp file, I can see that you're using some incorrect 
settings.  You've set rlist=rvdw even though you're using a shifted potential 
for van der Waals interactions.  Surely grompp should have warned you that this 
would lead to poor energy conservation.  Your solvent is probably heating up as 
a result and leading to the incorrect temperature.

-Justin

> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Tue, August 2, 2011 9:55:40 PM
> *Subject:* Re: [gmx-users] Problem with temperature and stochastic dynamics in 
>FEP
> 
> 
> 
> Sanku M wrote:
>  > 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.
>  >
>  >
> 
> I have never had such a problem when using sd.  I can always achieve the target 
>temperature within 0.5 K, if not exactly, so I do not believe there is an 
>inherent problem with sd.  Your first post indicated that your statistics were 
>collected over the entire timeframe, which will not be correct for reasons I 
>have already described.  The initial frames will represent unequilibrated data 
>that may skew the averages.  What if you analyze only the last half of the 
>time?  The last 1 ns?
> 
> -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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110802/9fc1897e/attachment.html>