[gmx-users] Energies in simulation
ppirzade at ucalgary.ca
Mon Jun 8 19:08:46 CEST 2009
To the best of my knowledge no, but how can I check that?
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
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:
> 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
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