Can this be modelled in NAMD

From: S.K. Ghosh (skg30_at_cam.ac.uk)
Date: Fri Aug 01 2008 - 11:38:38 CDT

Hi NAMD users,

I would like to know whether the following can be modelled in NAMD.

One end of my protein (of one monomer) will remain rigidly attached to a
surface which accelerates (from rest to ~10 m/s in ~10 ns) and the other
end (of another monomer) is attached to a microsphere which is three orders
of magnitude heavier than the protein. The inertial force of this sphere
will thus pull the protein. Can this inertial force be modelled without
actually putting this large microsphere but just considering the effect of
its mass on the motion of the protein.

And also for pulling the other end, if the pull is done with a soft spring
the velocity of the atom is much less than that of dummy atom and again if
the spring is too stiff the velocity is close to the dummy atom but the
fluctuation of force is too high. Is there any other way this 'hard' pull
can be modelled, perhaps without a dummy atom?

Your comments would be much appreciated.

Thanks,
Sourav

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