[gmx-users] about periodicity removal

Justin A. Lemkul jalemkul at vt.edu
Sat Feb 25 15:27:16 CET 2012

rama david wrote:
> Hi GROMACS friends,
>                          I am trying to put to peptide close to each other..
> with the help of -editconf  -ci and  -nmol option ,the peptide can be put
> randomly at different location, but they are far apart.
>      To solve problem I proceed as  follow...
> 1. I make gro file , with the -editconf I make box and put molecule in 
> center
>     I get the box vectors and center co-ordinates.
> 2. then again with the help of editconf I make a another box of same vectors
>    but slightly different center co-ordinates.(Distance is as per my 
> requirement)
> 3 Now have two gro files of box molecule ,having same box vectors and 
> different
>    center.
> 4 I converted both  gro files to pdb files ,and catenate them to make 
> single pdb file.
> 5  Now I get the two molecule close enough to form hydrogen bond..
>            but the problem is to convert it again into gro file and 
> generate topology

It is easier to not generate a topology from this file.  If the peptides are 
identical, run a coordinate file of *one* of them through pdb2gmx and obtain its 
topology.  Then simply update the number of protein molecules in the [molecules] 
directive to reflect that the new system has two.

> file , should I removed periodicity of molecule (As it showing the 
> periodic box in pymol)???
>     If it is , how to remove periodicity???

What periodicity do you want to remove?  You have two peptides in a box, there's 
nothing to do there.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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