[gmx-users] pbc

[Nuno R. L. Ferreira]

If you remove the pbc = xyz variable in the mdp, the run will be *exactly* the same. Because the default value for gmx is pbc = xyz.

Ah! And having the protein centered in the box, is a pos-production cosmetic effect, performed by trjconv and a combination of flags -pbc, -ur , -center. Though some MD programs do it automatically while performing the runs.

Regards
Nuno

 
  ----- Original Message ----- 
  From: Nancy Deng 
  To: Discussion list for GROMACS users 
  Sent: Tuesday, April 05, 2005 6:04 PM
  Subject: Re: [gmx-users] pbc


  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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