From: curcio (r.curcio_at_bioc.unizh.ch)
Date: Thu Oct 05 2006 - 10:59:10 CDT
as done for decaalanine by Schulten and coworkers I wanted to do some SMD
simulations pulling part of a (small) system first in one direction (from r_0
to r_1) and then in the opposite one (so from r_1 to r_0) using various
pulling velocities. The final aim is to see at which pulling velocity pulling
is a reversible proccess, i.e.
However, it is not clear to me (and not from the namd-tutorial files available
for the decaalanine case either) how the backward pulling has to be
In principle there are two possible ways:
1) starting backward pulling directly from the end of the forward pulling (so
rom r_1), i.e. using the restart files of the latter SMD-simulation and just
modifying the pulling direction to start the other SMD-run.
2) equilibrate the system at the final position of the forward pulling (so at
r_1) first and then start backward pulling from members of the
equilibration-ensemble, i.e. as done for the forward-pulling where
equilibration was done around r_0.
First test-runs have shown that these two ways don't give the same result,
i.e. force-extension curve, work-profiles etc. differ considerably.
Which of the two ways makes more sense (or is there yet another ("better")
Thanks and best regards,
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