[gmx-users] Regarding Position restraint and freezegroups

rahul seth rahul.seth.gromacs at gmail.com
Thu Aug 29 21:25:26 CEST 2013


I have been performing simulations with nanotubes. I read several entries
in the gromacs users forum regarding the correctness of the usage of the
freeze groups in simulations.
However, I am trying to perform NPT simulations at two different
temperatures using berendsen and parrinello-rahman barostat respectively
freezing the carbon nanotubes and position restraining them at the same

I am using refcoord-scaling = com

I do not have any information regarding the bonded interactions of the
carbon nanotubes since I am freezing and position restraining them anyways.
Interestingly, although Berendsen barostat keeps the diameter constant at a
fixed value the parrinello-rahman barostat changes the diameter of the
nanotube quite significantly at the higher temperatures. Can anyone explain
what is going on?

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