[gmx-users] Correction for the PBC!

[Justin A. Lemkul]

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
>>
>> ========================================
>> -- 
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at 
>> http://www.gromacs.org/Support/Mailing_Lists/Search 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
>>
>>
> 

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

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

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