AMBER Archive (2009)

Subject: [AMBER] problem in rmsd

From: Parimal Kar (
Date: Mon Mar 09 2009 - 22:18:48 CDT

Hi All,
     I am facing a weird problem while calculating the rmsd using
ptraj. I am doing the canonical simulation of TrpCage miniprotein at
325k. I followed the steps available online (provided by ross
Walker ). After heating the system to the desired temperature, I
created a pdb file and it looks reasonable. Then I performed 100ps
short canonical MD at this temperature and stored the configuration
in every 50 steps (ntwx=50). While I calculated the rmsd of the
trajectory from the experimental nmr structure, I found that 3rd &
4th snapshots give absurd rmsd (300+ AA). If I make ntwx=1, still I
found that 3rd & 4th snapshots gives absurd rmsd.
  Below is my input file for canonical MD simulation:

    325 K
   imin=0, irest=1, ntx=5,
   ntt=1, tempi=325.0, temp0=325.0,
   nstlim=200000, dt=0.0005,
   ntpr=50, ntwx=50,
   cut=999., ntf=2, ntc=2,
   ntb=0, igb=1,

Could any one please tell me what could be the reason?
Thanks advance

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