Den 2020-04-15 kl. 23:48, skrev Paolo Costa:
Dear Gromacs users,
I have a problem regarding force constant for bond stretching. By employing
VFFDT software, I got C-C bond stretching force constant (for Benzene,
B3LYP-6311++G*) equal to 383.23 kcal/ (mol A^2) which is equivalent to
160343 kj/ (mol nm^2). However when I look to the ffbonded.itp file of
Amber99.ff the CA-CA force constant value is 392459.2 kj/ (mol nm^2). It
seems that the value I got from VFFDT is somehow half than the one reported
in Amber force field.
Can somebody help me to figure out such issue?
Thanks a lot in advance for your help.
Vbond = (k/2) (r - r0)^2
Some methods do not use the division by two, so it can be a matter of
definition.
--
David van der Spoel, Ph.D.,
Professor of Biology
Uppsala University.
http://virtualchemistry.org
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