[gmx-users] Re: gmx-users Digest, Vol 102, Issue 112

Ali Alizadeh ali.alizadehmojarad at gmail.com
Thu Oct 18 13:08:09 CEST 2012

Dear Justin

On 10/18/12 6:45 AM, Ali Alizadeh wrote:
> Dear Justin
> Please check my commands, Are these correct, step by step?
> If these are correct then i will start my simulation with longer time,

   I really don't understand why you're invoking pdb2gmx three times.
You should
   only ever need to produce one topology.  You certainly do not need to run
    pdb2gmx after EM.  That makes no sense at all.  I suppose the effect is
    harmless, but confusing.


I use pdb2gmx for each step because i need .top for grompp.

In your opinion What can i do instead of?


More information about the gromacs.org_gmx-users mailing list