[gmx-users] clashes

[Dariush Mohammadyani]

Yes, you are right. I made a mistake to write an error:

[n0017:07436] *** Process received signal ***
[n0017:07436] Signal: Segmentation fault (11)
[n0017:07436] Signal code: Address not mapped (1)
[n0017:07436] Failing at address: 0x1d620d20



What do you mean for "Better energy minimization"?



Thanks,

Dariush




On Wed, Mar 14, 2012 at 10:08 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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