Hi everyone,
I am analysing a MD trajectory for average and snapshot structures using
cpptraj.
I have performed 50ns of MD with the following parameters. There are total
2500 frames in my trajectory.
ntx=1, irest=0, ntpr=1000, ntwx=10000, ntwr=100000,
ntf=2, ntb=2, cut=9.0, nsnb=10,
ntr=0,
imin=0, nstlim=25000000, dt=0.002
I am using following average.in script for calculating the average
structure.
/
trajin md.crd
average 2180-2500.pdb pdb start 2180 stop 2500 .1-66
strip:WAT
/
The pdb which I get after processing shows much more overlapped and
distorted structure.
I want to calculate the averages over frames 2180-2500 (nearly 40-50ns) in
batches of 5 or 10 frames per structure and also the overall average
structure.
What input should I design so as to get clear average structures with no
distortions?
Thanks in advance!!!!!
Mr. Prayagraj Fandilolu
Research Scholar,
Structural Bioinformatics Unit
Department of Biochemistry
Shivaji University, Kolhapur - 416004
(MS) India
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Received on Mon Jun 27 2016 - 04:00:02 PDT
