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
&cntrl
imin=0, irest=1, ntx=5,
ntt=1, tempi=325.0, temp0=325.0,
tautp=1.0
nstlim=200000, dt=0.0005,
ntpr=50, ntwx=50,
cut=999., ntf=2, ntc=2,
ntb=0, igb=1,
rgbmax=999.,
/
Could any one please tell me what could be the reason?
Thanks advance
Parimal
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Received on Wed Mar 11 2009 - 01:18:38 PDT
