[gmx-users] query regarding topology file

Jagannath Mondal jmondal at chem.wisc.edu
Mon Apr 9 04:01:11 CEST 2007

     I am a gromacs beginner. I am trying to simulate a non natural  
peptide. I have prepared a standalone  molecule .itp file for my  
molecule  and I have prepared a corresponding topology file 
(topol.top) which include the .itp file.

      Now, I used the genconf option to  replicate my molecule of my  
interest so that I can get 2 molecules . The genconf program gives  
rise to gro file in which all of the atoms has got 0 velocity. Can  
anyone suggest  what I should do to
  get a  random velocity for each of the atoms in my initial  gro  
file or is it  ok even if all the atoms has got 0 initial velocity  
and during simulation it gains a random velocity ?

  Yours sincerely
  Jagannath Mondal

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