[gmx-users] clashes

[Justin A. Lemkul]

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

-- 
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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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