[gmx-users] Re: DNA simulations

SatyaK mail2mvskumar at yahoo.com
Mon Jul 9 22:07:35 CEST 2012


 I followed below steps using VMD and GROMACS but something went wrong in
using GROMACS which I am not able to figure out. Appreciate your help.

 1. editconf -f initialfile.pdb -o initialfile.gro -d 0.2
 2. VMD: within 5 of nucleic
             $sel writepdb initialfile_updated.pdb
             $sel delete
      (initialfile_updated.pdb has only those molecules that are at a
distance of 5A)    

 3. I used GROMACS to convert back to .gro:editconf -f
initialfile_updated.pdb -o initialfile_updated.gro -d 0.2

 The coordinates in ininitialfile.gro and initialfile_updared.gro are
different. I quite don't understand the reason for the same.

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