[gmx-users] bonds braking

[Justin Lemkul]

On 10/15/12 8:40 AM, Eduardo Oliveira wrote:
> Thanks!
>
> So, if i understood correctly the correct workflow of trjconf?
>

I posted the link for two reasons: (1) so you would understand the nature of 
what was actually happening in the simulation and (2) so you would be aware of 
the solution.  In your case, a protein in water, the remedy is very easy:

trjconv -pbc mol -ur compact -center

Center on the protein.  You can apply various fitting operations afterwards if 
you like.

-Justin

> --------------------------------------------------------------------------------
> *De:* Justin Lemkul <jalemkul at vt.edu>
> *Para:* Eduardo Oliveira <eduardobio at yahoo.com.br>; Discussion list for GROMACS
> users <gmx-users at gromacs.org>
> *Enviadas:* Segunda-feira, 15 de Outubro de 2012 9:14
> *Assunto:* Re: [gmx-users] bonds braking
>
>
>
> On 10/15/12 8:09 AM, Eduardo Oliveira wrote:
>  > Hi,
>  >
>  > I'm having trouble simulating a protein kinase on water. During the
> simulation, the molecule moves towards the box limits and some residues apear on
> the other side. Almost like they are interacting with water molecules on
> different sides of the box. I'm on my third simulation and the problem persists.
> I've already tried changing the periodic conditions but with no success. Waht
> are your thoughts on that?
>  >
>  > For additional information:
>  > Before the dynamics step I performed 4 minimization steps then i did water
> dynamics and the entire system dynamics.
>  > Here is all the ".mdp " files.
>  >
>  > Sorry in advance for the long email.
>  >
>
> This is a perfectly normal consequence of PBC.
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================