[gmx-users] total energy of system is positive,MD normal ?

David van der Spoel spoel at xray.bmc.uu.se
Mon May 29 20:45:34 CEST 2006

linfu wrote:
> Dear all!
> My Simulation was done in decane and dmso. during analysis(g_energy), i find the energy of the whole system is positive
> not negative.however, fluctuation of temperature ,pressure and total energy is normal. Could anyone help me to figure out
> whether this MD is normal or not!
> Thank you in advance!
you are mainly interested in intermolecular energy. For this you have to 
calculate the intramolecular energy of the solvent (decane or dmso) and 
subtract that. Do a 1 molecule gas phase simulation, and subtract the 
Epot times the number of molecules in the solution. You will see that 
the interaction energy is negative.

> Jerry Lin
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
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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