[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
> 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
> gmx-users mailing list gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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
More information about the gromacs.org_gmx-users