On 8/14/13 6:42 PM, gg jj wrote:
Hi everybody.
I wonder how the "sign convention" of GROMACS (or better g_energy ) is: Is
U(state_i):= <E_tot (state_i)>_t correct or do i have to choose the other sign
U(state_i)= -1.0* <E_tot (state_i)>_t ? (<>_t denotes the time average)
I need the correct sign for further calculations since i need to add something
(-T\Delta S) to the difference of the inner energy of two states: \Delta
F=\Delta U -T\Delta S (for T=const)
There is no need to manipulate the sign. It's not even a Gromacs convention,
it's standard. Negative energy = net attraction, positive energy = net repulsion.
-Justin
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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