[gmx-users] Correction for the PBC!

[Justin A. Lemkul]

teklebrh at ualberta.ca wrote:
> 
> 
> Dear Justine,
> 
> No, I have 20 surfactants in my system in a pure solvent and try to see 
> the aggregation and adsorption properties of these molecules. I have run 
> them for 20ns. And now start to analyze my data.
> 
> Just in short I want to correct for periodicity! so that to get the 
> accurate result for my g_dist and g_rdf.
> 
> trjconv on the xxx.xtc.... Like
> 
> trjconv -f x_input.xtc -o x_out.xtc -b 19000 -e 20000 -s x_input.tpr 
> -pbc nojump
> 
> or I have to cluster it first.
> 

I'm sorry to say I have no definitive answer, but you should be able to 
determine this for yourself by watching the trajectory.  If a cluster forms, 
then clustering may be useful.  If you try to use -pbc cluster, but not all of 
your molecules are actually aggregating, then trjconv may loop infinitely.

Start with -pbc nojump, and perhaps iterations of -pbc mol and others, until you 
obtain a trajectory you can visualize and easily assess.  For the purposes of 
g_dist and g_rdf, PBC should be handled intrinsically.  There are other tools 
(like g_rms) for which PBC will make a difference, but not likely these two.

-Justin

> Rob
> 
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
> 
>  >
>  >
>  > teklebrh at ualberta.ca 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" <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
>  >>> 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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> 

-- 
========================================

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

========================================