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

Justin Lemkul jalemkul at vt.edu
Thu Oct 18 13:42:30 CEST 2012

On 10/18/12 7:08 AM, Ali Alizadeh wrote:
> 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.
>      -Justin
> I use pdb2gmx for each step because i need .top for grompp.
> In your opinion What can i do instead of?

I see no evidence that the topology changed between those steps.  Maybe there 
are other things going on that you're not saying, but from the commands posted, 
the multiple invocations of pdb2gmx seemed useless to me.  Once you build the 
system and set up the .top, it's fixed.  Again, I don't think this is at all 
related to your perceived problem.  I think your simulations are just an order 
of magnitude (at least) too short to be reliable.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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