[gmx-users] Energies in simulation

David van der Spoel spoel at xray.bmc.uu.se
Mon Jun 8 19:13:07 CEST 2009

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: 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 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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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