<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
<title></title>
</head>
<body text="#000000" bgcolor="#ffffff">
On 10/02/2011 10:54 AM, Rini Gupta wrote:
<blockquote
cite="mid:20110209235410.56548.qmail@f4mail206.rediffmail.com"
type="cite">Dear gmx users,<br>
<br>
I am using gromacs (version 4.0.7) first time<br>
to setup a 2-butoxyethanol-water simulation.<br>
I created topology and coordinate file for BE using AUTOMATED
TOPOLOGY BUILDER server.<br>
It created a topology file (for united atom) compatible with
GROMOS ffG53a6 forcefield.<br>
Then a generated a box containing 20 BE and 480 water molecules
using<br>
genbox.<br>
<br>
When I performed energy minimization followed by mdrun using NPT
ensemble.<br>
I get<br>
<br>
Potential Energy = -1.56616474544600e+04 <br>
Maximum force = 9.72854664927673e+02 on atom 910<br>
<br>
<br>
Then, I run for 200ps equlibration using NPT ensemble with
Berendsen <br>
thermostat and P coupling<br>
I want to use NVT ensemble for my calculations, so it is ok to
switch from NPT to NVT ensemble during equilibration?<br>
</blockquote>
<br>
Sure. See
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation">http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation</a><br>
<br>
<blockquote
cite="mid:20110209235410.56548.qmail@f4mail206.rediffmail.com"
type="cite">
First, I did equilibation for 200ps using NPT ensemble<br>
I get <br>
Total Energy Temperature Pressure (bar) Cons. rmsd ()<br>
-1.81617e+04 3.00167e+02 -4.32808e+00 0.00000e+00<br>
and,<br>
My box length changes from 2.7 nm to 2.6503 nm<br>
<br>
Then using state.cpt with mdrun I run for another 200ps using NVT
settings in .mpd file ( I turn off the P-coupling).<br>
<br>
I use the following commands:<br>
I regenerated new .tpr file <br>
grompp_d_mpi -f grompp.mdp -c confout.gro -p topol.top -o
topol.tpr<br>
<br>
mdrun_d_mpi -s topol.tpr -cpi state.cpt<br>
<br>
Simulation is completed with warning<br>
<br>
WARNING: The checkpoint state entries do not match the simulation,<br>
see the log file for details<br>
</blockquote>
<br>
OK and what did you learn from the .log file about this? (Probably,
it restarted from the coordinates of the confout.gro, which loses
precision and some of the value of your initial equilibration)<br>
<br>
<blockquote
cite="mid:20110209235410.56548.qmail@f4mail206.rediffmail.com"
type="cite">
and Pressure again increases up to 60 bar<br>
</blockquote>
<br>
No, it probably doesn't. See
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/Terminology/Pressure">http://www.gromacs.org/Documentation/Terminology/Pressure</a><br>
<br>
<blockquote
cite="mid:20110209235410.56548.qmail@f4mail206.rediffmail.com"
type="cite">
<br>
Total Energy Temperature Pressure (bar) Cons. rmsd ()<br>
-1.82304e+04 2.99992e+02 6.20706e+01 0.00000e+00<br>
<br>
<br>
I want to know if this is a right procedure for switching
ensemble.<br>
do i need to generate new velocities during second run using NVT
ensemble?<br>
If this is correct, how can i reach the target of Pressure 1 bar
using this approach?<br>
</blockquote>
<br>
See
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4">http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4</a><br>
<br>
<blockquote
cite="mid:20110209235410.56548.qmail@f4mail206.rediffmail.com"
type="cite">
I am using following topology file:<br>
Can anyone please tell me if this topology is o.k to use<br>
</blockquote>
<br>
It's syntactically correct because grompp doesn't complain. Whether
its a sensible model physics can sometimes be rejected off-the-cuff,
but can't really be confirmed without actually testing against some
other data.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:20110209235410.56548.qmail@f4mail206.rediffmail.com"
type="cite">
; Include forcefield parameters<br>
#include "ffG53a6.itp"<br>
<br>
[ moleculetype ]<br>
; Name nrexcl<br>
G269 3<br>
[ atoms ]<br>
; nr type resnr resid atom cgnr charge mass total_charge<br>
1 OE 1 G269 O 1 -0.345 15.9994<br>
2 CH2 1 G269 C 1 0.151 14.0270<br>
3 CH2 1 G269 C 1 0.194 14.0270 ; 0.000<br>
4 CH2 1 G269 C 2 0.231 14.0270<br>
5 OA 1 G269 O 2 -0.617 15.9994<br>
6 H 1 G269 H 2 0.386 1.0080 ; 0.000<br>
7 CH2 1 G269 C 3 -0.035 14.0270<br>
8 CH2 1 G269 C 3 0.143 14.0270<br>
9 CH3 1 G269 C 3 -0.108 15.0350 ; -0.000<br>
; total charge of the molecule: 0.000<br>
[ bonds ]<br>
; ai aj funct c0 c1<br>
1 2 2 0.1430 8.1800e+06<br>
1 3 2 0.1430 8.1800e+06<br>
2 4 2 0.1520 5.4300e+06<br>
3 7 2 0.1520 5.4300e+06<br>
4 5 2 0.1430 8.1800e+06<br>
5 6 2 0.1000 2.3200e+07<br>
7 8 2 0.1530 7.1500e+06<br>
8 9 2 0.1530 7.1500e+06<br>
[ pairs ]<br>
; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp<br>
1 5 1<br>
1 8 1<br>
2 6 1<br>
2 7 1<br>
3 4 1<br>
3 9 1<br>
[ angles ]<br>
; ai aj ak funct angle fc<br>
2 1 3 2 109.50 380.00<br>
1 2 4 2 109.50 320.00<br>
1 3 7 2 109.50 320.00<br>
2 4 5 2 111.00 530.00<br>
4 5 6 2 108.53 443.00<br>
3 7 8 2 111.00 530.00<br>
7 8 9 2 111.00 530.00<br>
[ dihedrals ]<br>
; GROMOS improper dihedrals<br>
; ai aj ak al funct angle fc<br>
[ dihedrals ]<br>
; ai aj ak al funct ph0 cp mult<br>
3 1 2 4 1 0.00 1.26 3<br>
2 1 3 7 1 0.00 1.26 3<br>
1 2 4 5 1 0.00 2.53 3<br>
1 3 7 8 1 0.00 3.77 3<br>
2 4 5 6 1 0.00 1.26 3<br>
3 7 8 9 1 0.00 3.77 3<br>
[ exclusions ]<br>
; ai aj funct ; GROMOS 1-4 exclusions<br>
<br>
<br>
<br>
<br>
; Include water topology<br>
#include "spce.itp"<br>
[ system ]<br>
; Name<br>
BE in Water<br>
<br>
[ molecules ]<br>
; Compound #mols<br>
G269 20<br>
SOL 480<br>
<br>
Please help me in this regard.<br>
<br>
Thanks and Regards,<br>
Rini<br>
<br>
----------------<br>
Dr. Rini Gupta<br>
Postdoctoral Fellow<br>
University of British Columbia<br>
Vancouver<br>
<br>
<br>
<br>
<table style="font-family: Verdana; font-size: 11px; line-height:
15px;" width="644" border="0" cellpadding="0" cellspacing="0"
height="57">
<tbody>
<tr>
<td><a moz-do-not-send="true"
href="http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle?"
target="_blank"><img moz-do-not-send="true"
src="http://sigads.rediff.com/RealMedia/ads/adstream_nx.ads/www.rediffmail.com/signatureline.htm@Middle"></a></td>
</tr>
</tbody>
</table>
</blockquote>
<br>
</body>
</html>