[gmx-users] Correction for the PBC!

teklebrh at ualberta.ca teklebrh at ualberta.ca
Tue Sep 14 07:11:31 CEST 2010

Dear Justine,

I just checked at the archive list and found out lots of information  
on how to correct for PBC! And if I understood it correctly is this  
the right way to follow...
“If you are trying to correct for periodicity for all species in the system
(protein and water) then a few iterations of trjconv may be necessary, i.e.
-center (on protein), followed by -pbc nojump or -pbc mol -ur compact.  Using
trjconv is a bit hit-or-miss, and just requires a bit of playing to  
get things working how you want them.”

trjconv –f xxx.xtc –o x_cluster.gro –b 19000 –e 20000 –pbc cluster

grompp –f xx.mdp –c x_cluster.gro –o x_cluster.tpr

trjconv –f xxx.xtc –o x_cluster.xtc –b 19000 –e 20000 –s  
xx_cluster.tpr –pbc nojump

Then I have to do anaysis on the new .tpr and .xtc...... is that correct....

Is this the right way to correct for periodicity... I took the idea  
from you and Chris. I have done the RDF and distance measurement but  
looks a bit off my RDF did not converge to 1. They recommend me to do  
PBC correction on my system which is run for 20ns. I am doing the  
analysis on the last 1ns (from 19-20 ns)

You suggestion is always helpful!


Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

> teklebrh at ualberta.ca wrote:
>> Dear Gromacs,
>> I want to correct the periodic boundry condition before analyzing  
>> my data, how do I perform that?
> Please see trjconv -h, as well as any of the thousands of posts in  
> the list archive related to this topic.
> -Justin
>> any suggest!
>> Rob
> -- 
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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