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

[Justin A. Lemkul]

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

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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