From: Victor Ovchinnikov (ovchinnv_at_mit.edu)
Date: Sat Jun 02 2007 - 16:08:55 CDT
I've been trying to use TMD capability that's available in NAMD to force
a conformational transition from one structure to another ( in explicit
water ). Mine is a large system with 15,000 protein atoms & ~100,000
In all my attempts, after an initial decrease of the RMSD toward the
target RMSD ( which I set to ~1.) the system becomes unstable & NAMD
dies with "atoms moving too fast."
I prepared the files as described in the UG; also experimented with a
large range of force costant values (1-100 kcal/mol/A^2 per atom); also
did the simulation over a variety of time periods (100-1000ps); lastly,
I tried forcing various subsets of the protein (e.g. just the backbone;
just the active site, etc)
In each case, the same error happens (at different times) and at this
point I'm inclined to think that this is not due to a bug.
Has anybody else done TMD in NAMD and, if so, with success?
Thanks for time & advice,
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