[gmx-users] Asymmetry in homo dimer simulation

Kavyashree M hmkvsri at gmail.com
Wed Dec 5 16:56:49 CET 2012

Dear users,

I have simulated a homodimer (both the chains with same number
of amino acids and in same configuration) using gromacs 453 in
OPLSAA force field at 2 different temperatures (say T1 and T2). It
was noticed that the rms fluctuation of chain A differs from chain B
in both the simulations. In one of the temperature (T2) the rmsf of the
protein is supposed to be more compared to the other (T1).

When I compare rmsf of chain A at T1 with chain A at T2 (similarly for
chain B). I observed that it shows opposite behaviour. ie chainB is
having increased fluctuation at T1 than at T2.

But actually i observed that the fluctuation of chain A at T1 resembles
the fluctuation of chain B at T2 (with increased values) and similarly
the fluctuations of chain B at T1 resembles that of chain A fluctuation
at T2 (with increased values).

Is this possible? or is there anything wrong?

Any suggestions would be of help.

Thank you

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