[gmx-users] How to modify or avoid some molecule clashing with another ?

Justin A. Lemkul jalemkul at vt.edu
Thu Dec 31 02:01:40 CET 2009

Chih-Ying Lin wrote:
> Hi
> After reading the log file and watching the trajectory movies(nstxout = 1),
> some molecule clashes with another in my simulation system.
> How can i avoid the situation happening again?
> How to modify the broken simulation?

Two options come to mind:

1. Re-generate the molecule coordinates by using the -seed option of genbox when 
inserting the molecules into the unit cell.
2. If the clash is between a ligand molecule and a solvent molecule, you could 
just delete the problematic water molecule and update the topology accordingly.



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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