[gmx-users] query regarding topology file
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 ?
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