[gmx-users] clashes

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 14 15:08:49 CET 2012

Dariush Mohammadyani wrote:
> Dear user,
> When I am using:
> genbox -cp confout.gro -cs water-1bar-303K.gro -vdwd 0.21 -o solvated.gro
> to add water in a coarse grained system, after running mdrun I am 
> getting "Syntax error" and it shows maybe the distances are so close or 
> there are some clashes.

I've never heard of mdrun throwing a syntax error.  Can you please copy and 
paste the complete error message from your terminal?

> Do you know how can I figure it out?
> Or actually if we have some clashes in system how we can correct them?

Better energy minimization typically solves bad atomic clashes.



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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