[email protected] wrote:
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)
Without context, I have no idea if what you've done is right. The clustering
algorithm is only really useful for the formation of clustered molecules (i.e.
micelles), so if you're trying to apply it to something else, I don't know that
it will work.
-Justin
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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--
========================================
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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