benzene in NAMD

From: Boyang Wang (pkuwangboyang_at_yahoo.com.cn)
Date: Sat May 14 2005 - 15:33:13 CDT

Hi all. I tried to put benzene in a water box and run dynamics using NAMD. But "benzene" was doing crazy sports and temperature rose extremely high.
      The problem was that it is very hard to define the rigid planar structure. If I use very high force constants for dihedral and improper, the dynamics becomes extremely unstable.
      And NAMD doesn't recognize delocalized Pi electrons and benzene is actually very hard to exist in NAMD.
      Any good advice?
      Thanks a lot.
Boyang,
Univ, Illinois at Chicago.
 

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