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On 29/10/2010 6:39 PM, vinothkumar mohanakrishnan wrote:
<blockquote
cite="mid:AANLkTinS714FbinqzxN9_hF6B-EecbzONyrB8JUccS9n@mail.gmail.com"
type="cite">I am using the semiisotropic pressure scaling because
i want the box size to remain the same as that of the original box
size in X and Y axis and want to change it only on the Z axis. I
am doing this because at a latter stage i want to create an
interface with organic solvent where i need the cross sections (X
and Y axis length) of both the box should be the same.<br>
<br>
what i should do now get the pressure of 1 bar?<br>
</blockquote>
<br>
7 +/- 500 *is* approximately 1 bar, and hardly any better an
approximation than 1 +/- 500. If you want lower fluctuations, use a
larger system and run for a much longer time. Or, since you'll have
to re-equilibrate once you combine the solvent boxes, don't bother.<br>
<br>
Mark<br>
<blockquote
cite="mid:AANLkTinS714FbinqzxN9_hF6B-EecbzONyrB8JUccS9n@mail.gmail.com"
type="cite"><br>
Has no one has got the pressure of water to be close to 1 bar in
GROMACS till now?<br>
<br>
Regards<br>
Vinoth<br>
<br>
<div class="gmail_quote">On Fri, Oct 29, 2010 at 12:54 PM, David
van der Spoel <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</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 2010-10-29 09.08, 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;">
<br>
Hi Mark<br>
<br>
I read the link before posting the question. even though
the fluctation<br>
is between 500-600 (as said in the link) bar the average
pressure is<br>
around 7.4 bar. my concern is the average pressure?.
Because at a latter<br>
stage i am going to combine this water box with another
organic solvent<br>
and i want to avoid any complications there.<br>
</blockquote>
<br>
</div>
Think again of what you just wrote. Your value is 7 +/- 500.
In fact according to normal statistical rules you should round
the value of 7 to 0. If you want more accurate number you
could increase the box size by a factor of 100.<br>
<br>
By the way, why are you using semiisotropic pressure scaling
in a water box?<br>
<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">
<br>
Regards<br>
Vinoth<br>
<br>
On Fri, Oct 29, 2010 at 12:22 PM, Mark Abraham <<a
moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
</div>
<div>
<div class="h5">
<mailto:<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>>
wrote:<br>
<br>
On 29/10/2010 5:48 PM, vinothkumar mohanakrishnan
wrote:<br>
<br>
Hi Gromacians<br>
<br>
I want to do equilibration of water (spc model)
first in the NVT<br>
ensemble and then in the NPT ensemble to maintain
a temperature<br>
of 300K and a pressure of 1 bar respectively. The
NVT<br>
equilibration works fine and the average
temperature turns out<br>
to be 299.229 K.<br>
<br>
Energy Average RMSD
Fluct.<br>
Drift Tot-Drift<br>
------------------------------<br>
-------------------------------------------------<br>
Temperature 299.229 10.3092
10.2463<br>
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<br>
pressure as 1 bar or atleast close to 1 bar
(between 1-1.4 bar).<br>
In the mdp file i used semiisotropic pressure
coupling type<br>
because i want to fix the length of the box same
on two axis as<br>
that of the original box size and want to change
it only on one<br>
axis. can any one tell me why iam not getting the
desired<br>
pressure of 1 bar?.<br>
<br>
<br>
This looks normal for a smallish water system over
100ps. See<br>
<a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Terminology/Pressure"
target="_blank">http://www.gromacs.org/Documentation/Terminology/Pressure</a><br>
<br>
Mark<br>
<br>
<br>
<br>
Energy Average RMSD
Fluct.<br>
Drift Tot-Drift<br>
-------------------------------------------------------------------------------<br>
Pressure (bar) 7.4339 574.052
573.574<br>
0.812129 81.2138<br>
<br>
Given below is my mdp file (NPT equilibration).
any help is<br>
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>
<br>
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<font color="#888888">
<br>
<br>
-- <br>
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