Yanmei Song wrote:
Dear Justin:
Thanks for your response. I got my force field parameters from PRODRG.
The system run well and I got a very reasonable density profile. Just
can not figure out what is the problem. I attached my itp file and gro
file. Would you please help me check what is the possible problem about
the force field parameters? I really appreciate your nice help!
Well, there are a ton of potential issues, but first and foremost you should
know (as I've said dozens of times on this list) raw PRODRG parameters are not
usually reliable. There are no ether functional groups to compare with the
force field, but I can see that your alcohol parameters look nothing like the
charges in any of the Gromos parameter sets. Your parameters aren't even
self-consistent - the alcohol at one end of the molecule has one set of charges,
and the other end is different! These parameters can't be right.
I don't know if this is the root cause of your problem, but it certainly makes
me question the reliability of anything you're doing.
-Justin
On Tue, Jan 26, 2010 at 3:02 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Yanmei Song wrote:
Dear Users:
I am in the process of setting up a new system. I have a
8.0*8.0*8.0 nm3 system which include 27800 molecules. When the
system approach equilibrium, I found the potential energy is
+3e5 (big positive number). Is this normal? Since based on my
experience, for systems in such size, the potential energy is
usually a big negative number? Does this mean that my force
field parameter or molecule structure have problems? Thanks in
advance!
A positive potential indicates repulsive interaction(s) is (are)
present in your system, i.e. you have clashes or have faulty
parameters. Energy minimization should converge to a nice, negative
number.
-Justin
--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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