Subject: Re: [gmx-users] GFP chromophore topology help

[Ramachandran G]

Thank you,
  Yes, i did energy minimization to the chromophore alone and it stays
stable....

The problem arise when i do the energy minimization to the
GFP-chromophore full system.
It clearly shows the atoms which is expected to connect the
negihbouring residues is flying apart.
I am still checking on the bond parameters to see whether i missed something.

Regards,
Rama

On Sat, Nov 13, 2010 at 12:54 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Gerrit Groenhof wrote:
>>
>> Can you perform a simulation of the chromophore alone? Does that stay
>> stable?
>>
>
> In that regard, some of the information on the following page may be useful:
>
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
>
> -Justin
>
> --
> ========================================
>
> 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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