<br>Hi Mark<br><br>I read the link before posting the question. even though the fluctation is between 500-600 (as said in the link) bar the average pressure is around 7.4 bar. my concern is the average pressure?. Because at a latter stage i am going to combine this water box with another organic solvent and i want to avoid any complications there.<br>
<br>Regards<br>Vinoth<br> <br><div class="gmail_quote">On Fri, Oct 29, 2010 at 12:22 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im">On 29/10/2010 5:48 PM, vinothkumar mohanakrishnan wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi Gromacians<br>
<br>
I want to do equilibration of water (spc model) first in the NVT ensemble and then in the NPT ensemble to maintain a temperature of 300K and a pressure of 1 bar respectively. The NVT equilibration works fine and the average temperature turns out to be 299.229 K.<br>
<br>
Energy Average RMSD Fluct. Drift Tot-Drift<br>
------------------------------<br>
-------------------------------------------------<br>
Temperature 299.229 10.3092 10.2463 0.0393873 3.93877<br>
Heat Capacity Cv: 12.494 J/mol K (factor = 0.00118698)<br>
<br>
when i do NPT equilibration i am not getting the desired pressure as 1 bar or atleast close to 1 bar (between 1-1.4 bar). In the mdp file i used semiisotropic pressure coupling type because i want to fix the length of the box same on two axis as that of the original box size and want to change it only on one axis. can any one tell me why iam not getting the desired pressure of 1 bar?.<br>
</blockquote>
<br></div>
This looks normal for a smallish water system over 100ps. See <a href="http://www.gromacs.org/Documentation/Terminology/Pressure" target="_blank">http://www.gromacs.org/Documentation/Terminology/Pressure</a><br>
<br>
Mark<div><div></div><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
Energy Average RMSD Fluct. Drift Tot-Drift<br>
-------------------------------------------------------------------------------<br>
Pressure (bar) 7.4339 574.052 573.574 0.812129 81.2138<br>
<br>
Given below is my mdp file (NPT equilibration). any help is highly appreciated.<br>
<br>
title = DCE NVT equilibration<br>
cpp = usr/bin/cpp<br>
integrator = md<br>
nsteps = 100000<br>
dt = 0.001<br>
nstxout = 100<br>
nstvout = 100<br>
nstenergy = 100<br>
nstlog = 100<br>
ns_type = grid<br>
nstlist = 1<br>
rlist = 1.0<br>
coulombtype = PME<br>
rcoulomb = 1.0<br>
vdwtype = Cut-off<br>
rvdw = 1.0<br>
pme_order = 4<br>
fourierspacing = 0.16<br>
pbc = xyz<br>
tcoupl = V-rescale<br>
tc-grps = system<br>
tau_t = 0.1<br>
ref_t = 300<br>
pcoupl = berendsen<br>
pcoupltype = semiisotropic<br>
tau_p = 0.5<br>
ref_p = 1.0 1.0<br>
compressibility = 0.0 4.5e-5<br>
DispCorr = Enerpres<br>
gen_vel = yes<br>
gen_temp = 300<br>
gen_seed = 173529<br>
<br>
Regards<br>
Vinoth<br>
<br>
</blockquote>
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