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

[David van der Spoel]

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