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<br />
<br />Dear Justine,
<br />
<br />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.
<br />
<br />Just in short I want to correct for periodicity! so that to get the accurate result for my g_dist and g_rdf.
<br />
<br />trjconv on the xxx.xtc.... Like
<br />
<br /><font color="#1012ff">trjconv -f x_input.xtc -o x_out.xtc -b 19000 -e 20000 -s x_input.tpr -pbc nojump</font>
<br />
<br />or I have to cluster it first.
<br />
<br />Rob
<br />
<br />Quoting "Justin A. Lemkul" <jalemkul@vt.edu>:
<br />
<br />>
<br />>
<br />> teklebrh@ualberta.ca wrote:
<br />>> Dear Justine,
<br />>>
<br />>> I just checked at the archive list and found out lots of information
<br />>> on how to correct for PBC! And if I understood it correctly is this
<br />>> the right way to follow...
<br />>> "If you are trying to correct for periodicity for all species in the system
<br />>> (protein and water) then a few iterations of trjconv may be necessary, i.e.
<br />>> -center (on protein), followed by -pbc nojump or -pbc mol -ur
<br />>> compact. Using
<br />>> trjconv is a bit hit-or-miss, and just requires a bit of playing to
<br />>> get things working how you want them."
<br />>>
<br />>> trjconv -f xxx.xtc -o x_cluster.gro -b 19000 -e 20000 -pbc cluster
<br />>>
<br />>> grompp -f xx.mdp -c x_cluster.gro -o x_cluster.tpr
<br />>>
<br />>> trjconv -f xxx.xtc -o x_cluster.xtc -b 19000 -e 20000 -s
<br />>> xx_cluster.tpr -pbc nojump
<br />>>
<br />>> Then I have to do anaysis on the new .tpr and .xtc...... is that correct....
<br />>>
<br />>> Is this the right way to correct for periodicity... I took the idea
<br />>> from you and Chris. I have done the RDF and distance measurement but
<br />>> looks a bit off my RDF did not converge to 1. They recommend me to
<br />>> do PBC correction on my system which is run for 20ns. I am doing the
<br />>> analysis on the last 1ns (from 19-20 ns)
<br />>>
<br />>
<br />> Without context, I have no idea if what you've done is right. The
<br />> clustering algorithm is only really useful for the formation of
<br />> clustered molecules (i.e. micelles), so if you're trying to apply it
<br />> to something else, I don't know that it will work.
<br />>
<br />> -Justin
<br />>
<br />>> You suggestion is always helpful!
<br />>>
<br />>> Rob
<br />>>
<br />>>
<br />>>
<br />>>
<br />>>
<br />>>
<br />>>
<br />>> Quoting "Justin A. Lemkul" <jalemkul@vt.edu>:
<br />>>
<br />>>>
<br />>>>
<br />>>> teklebrh@ualberta.ca wrote:
<br />>>>> Dear Gromacs,
<br />>>>>
<br />>>>> I want to correct the periodic boundry condition before analyzing
<br />>>>> my data, how do I perform that?
<br />>>>>
<br />>>>
<br />>>> Please see trjconv -h, as well as any of the thousands of posts in
<br />>>> the list archive related to this topic.
<br />>>>
<br />>>> -Justin
<br />>>>
<br />>>>> any suggest!
<br />>>>>
<br />>>>> Rob
<br />>>>
<br />>>> --
<br />>>> ========================================
<br />>>>
<br />>>> Justin A. Lemkul
<br />>>> Ph.D. Candidate
<br />>>> ICTAS Doctoral Scholar
<br />>>> MILES-IGERT Trainee
<br />>>> Department of Biochemistry
<br />>>> Virginia Tech
<br />>>> Blacksburg, VA
<br />>>> jalemkul[at]vt.edu | (540) 231-9080
<br />>>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a>
<br />>>>
<br />>>> ========================================
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<br />>>
<br />>
<br />> --
<br />> ========================================
<br />>
<br />> Justin A. Lemkul
<br />> Ph.D. Candidate
<br />> ICTAS Doctoral Scholar
<br />> MILES-IGERT Trainee
<br />> Department of Biochemistry
<br />> Virginia Tech
<br />> Blacksburg, VA
<br />> jalemkul[at]vt.edu | (540) 231-9080
<br />> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a>
<br />>
<br />> ========================================
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