[gmx-users] pbc

[Nancy Deng]

Dear all,

I am wondering if I remove the script line: "pbc = xyz" from my .mdp file, whether the program will automatically always center the protein in the solvent box. Appreciate you reply, please.

Thanks,

nancy
  ----- Original Message ----- 
  From: zjim 
  To: discussion list for gromacs users 
  Sent: Monday, April 04, 2005 5:58 PM
  Subject: Re: [gmx-users] trjconv



  maybe you needn't use "-n index.ndx", i always do as "trhconv -f *.trr -s *.tpr -o *.trr" it is ok. 
  > Hi all,
  > 
  > I use
  > > trjconv -f md.trr -s b4md.tpr -n index.ndx -o md_500ps.trr -e 500
  > to extract 500ps trajectory from 1ns trajectory.
  > 
  > but I found the output trr file is only one fourth of the original one.
  > 
  > what is deleted when I use this command?
  > 
  > thanks for your reply in advance.
  > 
  > Regards,
  > 
  > Jian Zou
  > 
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