Its basically a melting process and there is ample of published data on this (not related to gromacs though). The only reason for using freeze-dimensions was to avoid using pbc=xy in combination with walls since I thought the extra interactions due to the walls might make the simulations computationally intensive.<div>
<br></div><div>The data I have obtained from these runs doesn't seem to match with an npt MC simulation(fortran based in-house code) and the data from the MC simulation looks more credible when compared to published results.</div>
<div><br></div><div>Pooja <br><br><div class="gmail_quote">On Thu, Jul 15, 2010 at 10:21 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
<br>
Sai Pooja wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
1. Pressure<br>
For my initial configuration, I run a long nvt run. This gives me a pressure. Then I run an npt simulation at this prerssure. <br>
The idea is to do expansion runs(decrease pressure so that the system expands) to get a P vs density curve. <br>
For example, after I determine the pressure of the initial configuration from the long nvt run, say Pinit, I choose a set of pressures - Pinit, P1, P2...., PN s.t Pinit>P1,>P2...(eg. 74, 72, 70, 69.....50). Then for each pressure I run an npt simulation till the average converges.<br>
<br>
<br>
2. Freeze-dimension<br>
Is there a better alternative for running simulations for a planar system?<br>
<br>
</blockquote>
<br></div>
Maybe you want to use "pbc = xy" or walls? Is there any literature precedent for what you want to do, or perhaps an alternate procedure?<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Pooja<div><div></div><div class="h5"><br>
<br>
On Thu, Jul 15, 2010 at 10:02 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Sai Pooja wrote:<br>
<br>
<snip><br>
<br>
<br>
Do you run any equilibration prior to applying these parameters?<br>
Both N-H and P-R allow for wide fluctuations in temperature and<br>
pressure, respectively, which are exacerbated by systems that are<br>
not sufficiently equilibrated. Hence it could take a very<br>
long time<br>
if you do not equilibrate well using, i.e. a weak coupling<br>
scheme first.<br>
<br>
<br>
I usually start with a pressure nearby. For example, I start<br>
with a system which was equilibrated at p=71 and then run npt at<br>
p=69. Is that not sufficient?<br>
<br>
<br>
How do you determine the pressure before the simulation has begun?<br>
Moreover, freezing your system in one dimension can certainly<br>
complicate matters, since that is a non-equilibrium restraint on the<br>
dynamics. That could be a factor.<br>
<br>
-Justin<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
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</div></blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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