[gmx-users] Problem with simulation of Protein-DNA complex

[rarora at ens-cachan.fr]

Hi Tsjerk,
I have checked and re-checked the structure and it seems fine. I also  
made sure to minimise the starting structure really well after  
pdb2gmx. Although it did not achive required precision, but machine  
precision instead.
Also, the problem starts with the NVT, before that everythings seems  
to work fine.

Could there be any other source of error? I am not able to figure it out.

Many Thanks.

Quoting Tsjerk Wassenaar <tsjerkw at gmail.com>:

> Hi Rohit,
>
> Have you checked the atoms around 3460? It seems there's something wrong
> with your starting structure.
>
> Cheers,
>
> Tsjerk
>
> On Feb 9, 2012 2:09 PM, <rarora at ens-cachan.fr> wrote:
>
> Hi Lina,
>
> I am sorry, I think I forgot to mention that I did perform energy
> minimisation using Steep-Descent for 5000 steps, before NVT.
>
> I was so engrossed in other details that I forgot to mention it!
>
> Quoting lina <lina.lastname at gmail.com>: > On Thu, Feb 9, 2012 at 8:44 PM,
>  <rarora at ens-cachan.f...
> Bureau: +33 (0) 1 47 40 77 49
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>
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Rohit Arora
Laboratoire de Biologie et de Pharmacologie Génétique Appliquée (CNRS UMR
8113)
Ecole Normale Supérieure, Cachan
France
Bureau: +33 (0) 1 47 40 77 49
Portable: +33 (0) 6 23 85 12 46