[gmx-users] DrudeFF topology transfer from CHARMM to GROMACS

[Tomasz Piskorz]

Dear all,

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