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 <[email protected]>
*Para:* Eduardo Oliveira <[email protected]>; Discussion list for GROMACS
users <[email protected]>
*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
========================================
--
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