[gmx-users] query regarding topology file

Mark Abraham Mark.Abraham at anu.edu.au
Mon Apr 9 04:19:56 CEST 2007

Jagannath Mondal wrote:
> Hi,
>     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 ?

Please search the manual for "generate velocities". In general, 
searching the manual is the preferred course in these situations, so 
that you find out information which allows you to solve your problem or 
ask a refined question without requiring the use of other people's 
valuable time.


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