[gmx-users] Energies in simulation

David van der Spoel spoel at xray.bmc.uu.se
Mon Jun 8 19:06:05 CEST 2009

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 
> 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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