Dear all,
I ran a MD simulation using a truncated octahedron box. Then I imaged the
trajectory using the following input files for the ptraj command:
trajin ../name_md1.mdcrd
trajin ../name_md2.mdcrd
trajout ../name.pdb pdb
rms first out rms .P,O3',O5',C3',C4',C5'
center :1-24
image familiar
go
or
trajin ../name_md1.mdcrd
trajin ../name_md2.mdcrd
trajout ../name.pdb pdb
rms first out rms .P,O3',O5',C3',C4',C5'
center :1-24
image origin center familiar
go
The final trajectories show many overlap between water molecules.
So I tryied to use the IWRAP option in the MD run:
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 2,
pres0 = 1.0,
ntp = 1,
taup = 2.0,
cut = 10,
ntr = 0,
ntc = 2,
ntf = 2,
tempi = 300.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
iwrap = 1,
nscm = 1,
nstlim = 5000000,
dt = 0.002,
ntpr = 500,
ntwx = 100,
ntwr = 100
/
However, at the beginning of the simulation, my molecule is placed outside
the box and the center command of ptraj (please see below) doesn't modify
the solute position.
trajin ../name_md1.mdcrd
trajin ../name_md2.mdcrd
trajout ../PDB_traj/name_md_centre.pdb PDB
center :1-24
go
Have you any suggestion to overcome this problem?
Many thanks in advance,
Vincenzo
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Received on Wed Jan 10 2007 - 06:07:45 PST
