[gmx-users] about protein in periodic boundary condition..

rama david ramadavidgroup at gmail.com
Fri Feb 24 14:34:38 CET 2012

Hi GROMACS user,
                          With the help of command
genbox -ci <molecule name> -nmol <molecule no required>
 -o <out put file> -box <dimension >
 I get the desired no of added protein to cell.
 But I found that some part of protein is outside
the cell ..
   Is such system is good for further molecular dynamics study ...??

 After energy minimisation some time the protein is leaving the cell,
 Can I used these last frame for my further position restrained MD
  Thank you for help
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