<div class="gmail_quote"><div>Thanks Dr. Dallas Warren. I have plotted the picture of pressure with respect to simulation time, it is not fluctuation, it is monotonically decrease from about 500 to 3 bar, this is why I am confused.</div>
<div><br></div><div>If it really should take some time to converge the required pressure, my MD simulation is 4 ns, during the whole simulation time, the pressure keeps on decrease. (Will this pressure convergence take that long time?)</div>
<div><br></div><div>The initial box size is 12 ns *12 ns *12 ns, after the simulation, it turned out to be 52 * 52 *52 .</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
---------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 12 Oct 2009 14:32:19 +1100<br>
From: "Dallas B. Warren" <<a href="mailto:Dallas.Warren@pharm.monash.edu.au">Dallas.Warren@pharm.monash.edu.au</a>><br>
Subject: RE: [gmx-users] Pressure problem: pressure is too large<br>
during MDsimulation<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<89907EA1DCFB7548A431C13A270F9DD50859202D@prk-exch-01.vcp.local><br>
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<br>
Plot the fluctuations of the pressure with time for the simulation. Far<br>
better way I think to get an idea of what is going on with a property<br>
than just looking at values in a log file. Especially when you are<br>
starting out.<br>
<br>
<br>
<br>
With pressure coupling, it is not unusual to have a fluctuation of a<br>
hundred or so. And that is nothing to worry about, entirely normal<br>
behaviour to observe. And with such large fluctuations, the average<br>
pressure can deviate from the reference pressure. Of course, with more<br>
sample points and longer simulation time, it will get closer to the<br>
reference value.<br>
<br>
<br>
<br>
Catch ya,<br>
<br>
Dr. Dallas Warren<br>
Department of Pharmaceutical Biology<br>
Pharmacy and Pharmaceutical Sciences, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<a href="mailto:dallas.warren@pharm.monash.edu.au">dallas.warren@pharm.monash.edu.au</a><br>
+61 3 9903 9167<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble<br>
a nail.<br>
<br>
<br>
<br>
From: <a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a><br>
[mailto:<a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>] On Behalf Of Pan Wu<br>
Sent: Monday, 12 October 2009 2:20 PM<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Subject: [gmx-users] Pressure problem: pressure is too large during<br>
MDsimulation<br>
<br>
<br>
<br>
Hi gmx users,<br>
<br>
I am now simulating one protein with solvent, in all atom<br>
forcefield, gromacs official distributed version. The pressure of system<br>
seems to be unreasonable large, and during the whole process, the box<br>
keeps increasing.<br>
<br>
Here is how I set up the system,<br>
<br>
1. I solvate the proteini use spc216.gro, the log file shows:<br>
<br>
Output configuration contains 40990 atoms in 12386<br>
residues<br>
<br>
Volume: 412.593 (nm ^3)<br>
<br>
Density: 1015.79 g/L<br>
Number of SOL molecules: 13410<br>
<br>
<br>
<br>
2. Then I start to do MD with constrains (40 ps), then MD without<br>
constrains.<br>
<br>
The md.log shows pressure keeps decrease, start from<br>
5.79 e+02 until at last to about 3.14e+00, so you can see how large the<br>
box size is enlarged.<br>
<br>
However in my setup, what I use for P-coupling is the same:<br>
<br>
Pcoupl = Berendsen<br>
<br>
Pcoupltype = isotropic<br>
<br>
tau_p = 0.5<br>
<br>
compressibility = 4.5e-5<br>
<br>
ref_p = 1.0<br>
<br>
<br>
<br>
my integral step size is 1fs, so the tau_p = 0.5 ps should be<br>
enough. Also I checked the temperature, it is constant during the MD<br>
process. (303K)<br>
<br>
<br>
<br>
So from these setup process, I think: the density is correct<br>
for solvent water and system; the compressibility is chosen as for<br>
standard water, the ref_p is chosen as 1.0. Why the pressure is so<br>
large?<br>
<br>
<br>
<br>
Thank you in advance!<br>
--<br>
Sincerely<br>
=================================<br>
Pan Wu<br>
Graduate Student in Department of Chemistry<br>
Duke University<br>
124 Science Drive<br>
5301 French Family Science Center<br>
Durham, NC 27708<br>
Phone: (919) 660-1583<br>
=================================<br>
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</blockquote></div><br><br clear="all"><br>-- <br>Sincerely<br>=================================<br>Pan Wu<br>Graduate Student in Department of Chemistry<br>Duke University<br>124 Science Drive<br>5301 French Family Science Center<br>
Durham, NC 27708<br>Phone: (919) 660-1583<br>=================================<br><br>