Den 2020-03-15 kl. 00:59, skrev 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
The baseline oof the potential energy is not a meaningful number in
classical force fields. You have to subtract 100 times the energy of the
monomer, then you will have the enthalpy of vaporization (+/- kT) which
you can compare to experiment.
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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