[gmx-users] potential energy doesn't have negative value

[Justin Lemkul]

On 3/14/20 7:15 PM, Afsane Farhadi wrote:
> I generate a box of 100 molecules of methyldiethanolamine with insert-molecules command .I downloaded its itp file from ATB server. I think that forcefield is gromos . after an energy minimization the potential energy is positive.  the mdp file is attached.

The mailing list does not accept attachments.

ATB does produce GROMOS-compatible force fields, but it is always up to 
the user to determine if the parameters are suitable. A positive 
potential energy means that the intermolecular interactions are weak 
compared to the intramolecular (bonded) interactions. You can use gmx 
energy or look in the .log file to see the various contributions to the 
total potential energy.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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