[gmx-users] multiple molecules in a box

Justin A. Lemkul jalemkul at vt.edu
Mon Jan 23 17:01:42 CET 2012

Turgay Cakmak wrote:
> Hi gromacs users,
> I have two different molecules, lets say A and B. I want to put 5 A 
> molecules and 5 B molecules in the same box.
> I carried out the following steps.
>    1)  For both A and B, I used *genbox* with *-nmol* flag separetely 
> and obtained the A_multiple and the B_multiple structure files.
>    2)  Using *cat* command, I concatanated two structure files 
> (A_multiple, B_multiple) to get system.gro.
>    3)  Using the *pdb2gmx*, I got conf.gro and topol.top of system..
> But, I am not sure if this is the correct way? Because, when I look the 
> conf.gro at VMD, I saw that some part of the A molecule and B molecule 
> had overlapped.
> Could anybody help me please?

An alternate procedure:

1. Run pdb2gmx on a single molecule of A and a single molecule of B
2. Convert the two resulting .top files into .itp files (see the manual or wiki 
for the differences) and construct a simple .top that #includes these
3. Build your system for molecule A as you did before
4. Insert 5 molecules of B into the A system to avoid clashes

This way you avoid a lot of topological redundancy and eliminate clashes.


> Turgay


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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