[gmx-users] "Sign convention" g_energy total energies

[Justin Lemkul]

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
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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