[gmx-users] Energies in simulation

[Payman Pirzadeh]

To the best of my knowledge no, but how can I check that?


-----Original Message-----
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:
> 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.
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