[gmx-users] Block calculation

Kelsy Yuan kelsy.yuan at gmail.com
Thu Dec 22 22:26:06 CET 2016


I am working on a system that contains a mica block and some stearic acid
molecules. The mica block is considered as a frozen group, and we are only
interested in calculating the dynamics of the stearic acid molecules on top
of it. When I try to minimize the energy of the system by using grompp,
many errors occurred according to the force field of mica. Since all I need
is an ionic surface for stearic acids and I do not interested in the
dynamics of mica, I wonder is it possible to skip the force field part of
mica? According to the Gromacs Manual, the frozen group keep stationary in
dynamics, so I wonder can gromacs do calculation without checking the force
field of the frozen group?

Thanks in advance,

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