[gmx-users] multiple molecule interaction

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 21 13:39:28 CEST 2011

smriti Sebastian wrote:
> hi all,
> I am new to GROMACS.I would like to know how we will simulate putting 
> more than two or more molecules of same proteins inside the box and do 
> simulation?Is there any possibility to replace 100 atoms or so of 
> solvent with proteins?

You can use editconf -center to place any molecule anywhere within a box.  Do 
this as many times as you need and concatenate the resulting coordinate files.

Regarding replacing solvent with protein, that's a bit difficult.  The genbox 
mechanism does the opposite - when provided with the coordinates of a solute, it 
adds solvent into the box and removes solvent molecules when they overlap with 
the solute.  I do not believe there is a targeted way to remove a specific 
number of water molecules and replace them with a protein, but genbox should 
have the same effect.



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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