From: Shulin Zhuang (shulin.zhuang_at_gmail.com)
Date: Thu Mar 23 2006 - 23:58:15 CST
When I use namd2.6b1 at the linux cluster to heat my protein, I get a
problem. The progein is solvated using vmd for 8 angstrom. However, the
earlies energy minimization stage runs well , after the minimization stage,
I run 7000 step to heat the protein. the time step is 2 ps. at steps 3200,
the erros arise:
WRITING COORDINATES TO DCD FILE AT STEP 3200
ERROR: Atom 4361 velocity is 6301.42 17609.1 -8680.79 (limit is 5000)
ERROR: Atom 4991 velocity is -5977.04 -16855.7 8820.4 (limit is 5000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Exiting prematurely.
The atom 4361 in my protein is the HB2 of HSE residue, and 4991, HE2 of MET
ATOM 4361 HB2 HSE 290
ATOM 4991 HE2 MET 329
The configuration file is attached.
Wish you would give me any suggestions.
-- Shulin Zhuang Chemistry Department Zhejiang University PRC shulin.zhuang_at_gmail.com
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