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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
