[gmx-users] DrudeFF topology transfer from CHARMM to GROMACS
tomasz.k.piskorz at gmail.com
Wed May 31 13:06:28 CEST 2017
I would like to simulate cyclohexane using Drude FF in GROMACS. I've seen
that the topology is already available in CHARMM-DrudeFF and I would like
to transfer it to GROMACS. However, I don't know how to calculate the
charge of Drude particle, which is required by topology in GROMACS. Does
anyone know how to do it?
Atomic polarizability can be described by equation:
alpha = (q_D)^2/k,
where k = 418400 kJ/(mol*nm^2) and alpha is given in CHARMM topology (i.g.
for O in glycine alpha=0.000651 nm^3). However, when I try to calculate the
charge I always get a wrong result. Is this question which I should use or
there is something more which I don't take under consideration?
With kind regards,
Tomasz K. Piskorz
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