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>Regards<br>Vinoth<br><br><div class="gmail_quote">
On Fri, Oct 29, 2010 at 4:21 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;">
<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 Mark<br>
<br><div class="im">
How come 7 +/- 500 bar is approximately 1 bar. Can you explain it more clearly? It will be of more useful to me to understand the concept.<br>
<br>
</div></blockquote>
<br>
Suppose you do two simulations. In one, the result is 7+/-500 and in the other, the result is 1+/-500. Even though the latter achieves the preferred result (average pressure of 1 bar), statistically, there is no difference between these two results because of the huge standard deviations in the data.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
One more thing, density (from g_energy command) of water is found to low (expected 1000) after NPT is equilibration. why? given below is my average density value. Can i proceed with this density value?<br>
<br>
Energy Average RMSD Fluct. Drift Tot-Drift<br>
-------------------------------------------------------------------------------<br>
Density (SI) 979.37 14.3238 14.2431 -0.0525784 -5.25789<br>
</blockquote>
<br></div>
Real water and SPC water are different. I don't know that there is any water model out there that perfectly reproduces all the 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 same box dimensions for two different systems in order to concatenate them and make an interfacial system? It would be far easier to create the organic phase, extend the box in z, and then solvate with genbox.<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;">
<br>
Regards<br>
Vinoth<div class="im"><br>
<br>
On Fri, Oct 29, 2010 at 2:06 PM, Mark Abraham <<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>>> wrote:<br>
<br>
On 29/10/2010 6:39 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;">
I am using the semiisotropic pressure scaling because i want the<br>
box size to remain the same as that of the original box size in X<br>
and Y axis and want to change it only on the Z axis. I am doing<br>
this because at a latter stage i want to create an 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>
</blockquote>
<br>
7 +/- 500 *is* approximately 1 bar, and hardly any better an<br>
approximation than 1 +/- 500. If you want lower fluctuations, use a<br>
larger system and run for a much longer time. Or, since you'll have<br>
to re-equilibrate once you combine the solvent boxes, don't bother.<br>
<br>
Mark<br>
<br>
</div><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>
Has no one has got the pressure of water to be close to 1 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></div><div><div></div><div class="h5">
<<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>>> 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 though<br>
the fluctation<br>
is between 500-600 (as said in the link) bar the 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 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 +/- 500.<br>
In fact according to normal statistical rules you 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 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> <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 mohanakrishnan wrote:<br>
<br>
Hi Gromacians<br>
<br>
I want to do equilibration of water (spc model)<br>
first in the NVT<br>
ensemble and then in the NPT ensemble to maintain a<br>
temperature<br>
of 300K and a pressure of 1 bar 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 (factor =<br>
0.00118698)<br>
<br>
when i do NPT equilibration i am not 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 box same on<br>
two axis as<br>
that of the original box size and want to change it<br>
only on one<br>
axis. can any one tell me why iam not 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 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>
--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>><br>
<br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at<br>
<a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a><br>
before posting!<br>
Please don't post (un)subscribe requests to the list.<br>
Use the www<br>
interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>>.<br>
<br>
Can't post? Read<br>
<a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
<br>
<br>
<br>
-- David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br></div></div>
<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>> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><div class="im">
<br>
<br>
-- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div><div class="im">
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at<br>
<a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before<br>
posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
<br>
</div></blockquote><div class="im">
<br>
<br>
--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at<br>
<a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
<br>
</div></blockquote>
<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>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<div><div></div><div class="h5"><br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br>