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!
Rob
Quoting "Justin A. Lemkul" <[email protected]>:
[email protected] 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
MILES-IGERT Trainee
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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