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.
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