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Dear Experts,
As I have known, image command of program PTRAJ makes all molecules to be in
the box leading to a good visual of simulation box and there is no effect
with any energy. However, I have extracted WAT residues around DNA within 5
Angstrom from original trajectory and from trajectory performed image
command. I found that the number of water molecules obtained from the both
trajectory files are different. This means that if I want to do anything
with WAT residues, I should use original trajectory file, right?
By the way, if I run MD with iwrap=0 or iwrap=1, I should obtain the
difference structure of solvent. Is it true?
Any suggestion is appreciated.
Many thanks in advance.
Xiaolin
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Received on Wed Oct 17 2001 - 05:22:20 PDT
