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On 4/08/2011 1:51 AM, Sanku M wrote:
<blockquote
cite="mid:1312386690.8837.YahooMailRC@web114416.mail.gq1.yahoo.com"
type="cite">
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<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>
</blockquote>
<br>
... and the tau_t issue I mentioned?<br>
<br>
Mark<br>
<br>
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<div>Sanku</div>
<div style="font-family:times new roman, new york, times,
serif;font-size:12pt"><br>
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<hr size="1"><b><span style="font-weight: bold;">From:</span></b>
Mark Abraham <a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a><br>
<b><span style="font-weight: bold;">To:</span></b>
Discussion list for GROMACS users
<a class="moz-txt-link-rfc2396E" 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 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>
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On 3/08/2011 2:23 PM, Sanku M wrote:
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<div><br>
</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>
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<hr size="1"><b><span style="font-weight:bold;">From:</span></b>
Justin A. Lemkul <a moz-do-not-send="true"
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<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
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> *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>
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