[gmx-users] Replacing molecules in .gro coordinate file

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 24 16:17:58 CET 2008

Waipot Ngamsaad wrote:
> Hello Guys,
> I am a newbie for GROMACS and MD also. I apologize if this is a stupid 
> question :).
> Supposed I have a .gro file of 38 molecules of A which are already in 
> equilibrated conformations. Now I want to transform 15 molecules of A 
> into B therefore I will have the binary mixture of A/B with 13:15 molar 
> ratio in the final structure. How can I do this? Any suggestions will be 
> appreciated.

Depending on how different A and B are, you may be able to complete this task 
with a text editor.

If they are very different, I don't know if there is an easy solution apart from 
rebuilding the system.  You could, for example, have a system with 13 A and 
insert 15 B using genbox -cp a.gro -ci b.gro -nmol 15


> Have a great day
> Waipot
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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