AMBER Archive (2007)

Subject: AMBER: image command

From: venditti2_at_unisi.it
Date: Tue Jan 09 2007 - 08:09:07 CST

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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