Payman Pirzadeh wrote:
To the best of my knowledge no, but how can I check that?
A. read the original paper: is your topology correct? Are the simulation
parameters the same?
B. post the itp file here and mdp file and specify energy and expected
energy. How about energy units?
-----Original Message-----
From: [email protected] [mailto:[email protected]]
On Behalf Of David van der Spoel
Sent: June 8, 2009 11:06 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote:
Hi,
I am using my own water model which I developed its .itp file. When
simulation is done after 1ns and energy is kinetic and potential
energies are analyzed, the kinetic value is almost OK, but the potential
energy is almost half of the value reported in literature and another MD
code that I am currently using. I double-checked the parameters I gave
in the .itp with TIP4P and TIP5P to make sure everything is correct in
format and unit. But I can not figure out the problem. Any ideas?
Is there any self-energy involved (i.e. a monomer energy that yo have to
subtract)?
Payman
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David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
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