[gmx-users] Correction for the PBC!

[teklebrh at ualberta.ca]

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. 

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[1] 
>>> 
>>> ======================================== 
>>> -- 
>>> gmx-users mailing list gmx-users at gromacs.org 
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users[2] 
>>> Please search the archive at 
>>> http://www.gromacs.org/Support/Mailing_Lists/Search[3] before posting! 
>>> Please don't post (un)subscribe requests to the list. Use the www 
>>> interface or send it to gmx-users-request at gromacs.org. 
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists[4] 
>>> 
>>> 
>> 
> 
> -- 
> ======================================== 
> 
> 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[5] 
> 
> ======================================== 
> -- 
> gmx-users mailing list gmx-users at gromacs.org 
> http://lists.gromacs.org/mailman/listinfo/gmx-users[6] 
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search[7] before posting! 
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org. 
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists[8] 
> 
> 



Links:
------
[1] http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
[2] http://lists.gromacs.org/mailman/listinfo/gmx-users
[3] http://www.gromacs.org/Support/Mailing_Lists/Search
[4] http://www.gromacs.org/Support/Mailing_Lists
[5] http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
[6] http://lists.gromacs.org/mailman/listinfo/gmx-users
[7] http://www.gromacs.org/Support/Mailing_Lists/Search
[8] http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100914/b82f86bb/attachment.html>