<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:12pt"><div>Hi Mark and Justin,</div><div> 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.</div><div>Only reducing the time step does help ( even if rvdw=rlist) to get average temperature to 300K.</div><div>Sanku</div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><br><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Mark Abraham <Mark.Abraham@anu.edu.au><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight:
bold;">Sent:</span></b> Tue, August 2, 2011 11:46:21 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP<br></font><br>
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On 3/08/2011 2:23 PM, Sanku M wrote:
<blockquote type="cite">
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</div>
<div style="font-family:times new roman, new york, times, serif;font-size:12pt;"> 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.</div>
<div style="font-family:times new roman, new york, times, serif;font-size:12pt;">Still Not sure why md integrator still
could 300K average temperature using 0.002 ps as time-step.</div>
</div>
</blockquote>
<br>
So your integration step was too large to conserve energy. There
have been two suggestions made about why that might be true. Have
you investigated them?<br>
<br>
Mark<br>
<br>
<blockquote type="cite">
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<div style="font-family:arial, helvetica, sans-serif;font-size:13px;"><font face="Tahoma" size="2">
<hr size="1"><b><span style="font-weight:bold;">From:</span></b>
Justin A. Lemkul <a rel="nofollow" class="moz-txt-link-rfc2396E" ymailto="mailto:jalemkul@vt.edu" target="_blank" href="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></a><br>
<b><span style="font-weight:bold;">To:</span></b>
Discussion list for GROMACS users
<a rel="nofollow" class="moz-txt-link-rfc2396E" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a><br>
<b><span style="font-weight:bold;">Sent:</span></b> Tue,
August 2, 2011 10:16:17 PM<br>
<b><span style="font-weight:bold;">Subject:</span></b>
Re: [gmx-users] Problem with temperature and stochastic
dynamics in FEP<br>
</font><br>
<br>
<br>
Sanku M wrote:<br>
> Hi Justin,<br>
> I did calculate the average temperature using last 2
ns of the 8ns data. It is still same 303K. <br>
> <br>
<br>
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.<br>
<br>
-Justin<br>
<br>
>
------------------------------------------------------------------------<br>
> *From:* Justin A. Lemkul <<a rel="nofollow" ymailto="mailto:jalemkul@vt.edu" target="_blank" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
> *To:* Discussion list for GROMACS users <<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
> *Sent:* Tue, August 2, 2011 9:55:40 PM<br>
> *Subject:* Re: [gmx-users] Problem with temperature and
stochastic dynamics in FEP<br>
> <br>
> <br>
> <br>
> Sanku M wrote:<br>
> > 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.<br>
> > The problem arises when sd integrator is used.<br>
> > 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 .<br>
> ><br>
> > 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.<br>
> ><br>
> ><br>
> <br>
> 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?<br>
> <br>
> -Justin<br>
> <br>
> -- ========================================<br>
> <br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
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Virginia Tech<br>
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