Hi Justin<br><br>Thank you. One more question regarding the Compressibility value usage. can i use the Compressibility value of water (4.5e-5) for the NPT equilibration of organic liquids (say DCE)? Is it resonable? <br><br>
It was said in the gromacs mailing archive that for all liquids one can use the Compressibility value of water. (<a href="http://www.mail-archive.com/gmx-users@gromacs.org/msg01245.html">http://www.mail-archive.com/gmx-users@gromacs.org/msg01245.html</a>)<br>
<br>Regards<br>Vinoth<br><br><div class="gmail_quote">On Fri, Oct 29, 2010 at 4:42 PM, 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: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im"><br>
<br>
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 Justin<br>
<br>
Thank you for your comments. Yes i want to concatenate two systems such that their cross sections are same ( X and Y axis length are same for both the boxes) allowing only the Z axis to change. The above procedure was employed in the literature and latter they combined two boxes.<br>
<br>
what i want to know ultimately is can i go ahead with this pressure ( i have no problem with temperature and density) for water to create an interface by combining two boxes?<br>
<br>
<br>
</blockquote>
<br></div>
Yes, it's fine. Regardless, you're going to have to do more equilibration after you've assembled the system.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Regards<br>
Vinoth<div><div></div><div class="h5"><br>
<br>
On Fri, Oct 29, 2010 at 4:21 PM, 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>
vinothkumar mohanakrishnan wrote:<br>
<br>
Hi Mark<br>
<br>
How come 7 +/- 500 bar is approximately 1 bar. Can you explain<br>
it more clearly? It will be of more useful to me to understand<br>
the concept.<br>
<br>
<br>
Suppose you do two simulations. In one, the result is 7+/-500 and<br>
in the other, the result is 1+/-500. Even though the latter<br>
achieves the preferred result (average pressure of 1 bar),<br>
statistically, there is no difference between these two results<br>
because of the huge standard deviations in the data.<br>
<br>
<br>
One more thing, density (from g_energy command) of water is<br>
found to low (expected 1000) after NPT is equilibration. why?<br>
given below is my average density value. Can i proceed with this<br>
density value?<br>
<br>
Energy Average RMSD Fluct. Drift Tot-Drift<br>
-------------------------------------------------------------------------------<br>
Density (SI) 979.37 14.3238 14.2431<br>
-0.0525784 -5.25789<br>
<br>
<br>
Real water and SPC water are different. I don't know that there is<br>
any water model out there that perfectly reproduces all the<br>
properties of water. A density around 980 sounds about right for SPC.<br>
<br>
A comment on your previous approach: you're hoping to achieve the<br>
same box dimensions for two different systems in order to<br>
concatenate them and make an interfacial system? It would be far<br>
easier to create the organic phase, extend the box in z, and then<br>
solvate with genbox.<br>
<br>
-Justin<br>
<br>
<br>
Regards<br>
Vinoth<br>
<br>
<br>
On Fri, Oct 29, 2010 at 2:06 PM, Mark Abraham<br>
<<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br></div></div><div class="im">
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>>> wrote:<br>
<br></div><div><div></div><div class="h5">
On 29/10/2010 6:39 PM, vinothkumar mohanakrishnan wrote:<br>
<br>
I am using the semiisotropic pressure scaling because i<br>
want the<br>
box size to remain the same as that of the original box<br>
size in X<br>
and Y axis and want to change it only on the Z axis. I am<br>
doing<br>
this because at a latter stage i want to create an<br>
interface with<br>
organic solvent where i need the cross sections (X and Y axis<br>
length) of both the box should be the same.<br>
<br>
what i should do now get the pressure of 1 bar?<br>
<br>
<br>
7 +/- 500 *is* approximately 1 bar, and hardly any better an<br>
approximation than 1 +/- 500. If you want lower fluctuations,<br>
use a<br>
larger system and run for a much longer time. Or, since<br>
you'll have<br>
to re-equilibrate once you combine the solvent boxes, don't<br>
bother.<br>
<br>
Mark<br>
<br>
<br>
Has no one has got the pressure of water to be close to 1<br>
bar in<br>
GROMACS till now?<br>
<br>
Regards<br>
Vinoth<br>
<br>
On Fri, Oct 29, 2010 at 12:54 PM, David van der Spoel<br>
<<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>><br></div></div>
<mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>>>><div><div></div><div class="h5">
<br>
wrote:<br>
<br>
On 2010-10-29 09.08, vinothkumar mohanakrishnan wrote:<br>
<br>
<br>
Hi Mark<br>
<br>
I read the link before posting the question. even<br>
though<br>
the fluctation<br>
is between 500-600 (as said in the link) bar the<br>
average<br>
pressure is<br>
around 7.4 bar. my concern is the average pressure?.<br>
Because at a latter<br>
stage i am going to combine this water box with<br>
another<br>
organic solvent<br>
and i want to avoid any complications there.<br>
<br>
<br>
Think again of what you just wrote. Your value is 7<br>
+/- 500.<br>
In fact according to normal statistical rules you<br>
should round<br>
the value of 7 to 0. If you want more accurate number you<br>
could increase the box size by a factor of 100.<br>
<br>
By the way, why are you using semiisotropic pressure<br>
scaling<br>
in a water box?<br>
<br>
<br>
Regards<br>
Vinoth<br>
<br>
On Fri, Oct 29, 2010 at 12:22 PM, Mark Abraham<br>
<<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a 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<br>
mohanakrishnan wrote:<br>
<br>
Hi Gromacians<br>
<br>
I want to do equilibration of water (spc<br>
model)<br>
first in the NVT<br>
ensemble and then in the NPT ensemble to<br>
maintain a<br>
temperature<br>
of 300K and a pressure of 1 bar<br>
respectively. The NVT<br>
equilibration works fine and the average<br>
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<br>
(factor =<br>
0.00118698)<br>
<br>
when i do NPT equilibration i am not<br>
getting the<br>
desired<br>
pressure as 1 bar or atleast close to 1 bar<br>
(between 1-1.4 bar).<br>
In the mdp file i used semiisotropic pressure<br>
coupling type<br>
because i want to fix the length of the<br>
box same on<br>
two axis as<br>
that of the original box size and want to<br>
change it<br>
only on one<br>
axis. can any one tell me why iam not<br>
getting the<br>
desired<br>
pressure of 1 bar?.<br>
<br>
<br>
This looks normal for a smallish water system over<br>
100ps. See<br>
<a 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<br>
equilibration). any<br>
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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