Re: SMD

From: Leandro Martínez (leandromartinez98_at_gmail.com)
Date: Thu Sep 15 2011 - 07:21:15 CDT

The physical meaning is that the ligand is moving along the path
spontaneously faster than the SMD spring, so that the SMD restraint is
actually holding it in back. It may happen, although only if your pulling
velocity is very small (which is good) and the path is indeed very
favorable. But, note, if that happens you should observe the movement of the
ligand in that direction even in an equilibrium run (without SMD).

Leandro.

On Thu, Sep 15, 2011 at 9:12 AM, Jacopo Sgrignani <sgrigna_at_sissa.it> wrote:

> Dear All
> I'm performing SMD simulations and I have a question about the force
> applied to pull out a ligand from a protein.
> Actually, analyzing the results of my simulations, they seem correct and
> the directions of the ligand exit are consistent with
> the directions I have specified in the input file.
>
> However for one of the 4 simulations, during the first 300 ps, the force
> applied is negative.
> What does it mean?
>
> I think this is the favoured exit pathway, however I would like to be sure
> that it has a physical meaning, and that It is not related with my tecnical
> errors.
>
> Thanks
>
> Jacopo
>
>
----------------------------------------------------
Leandro Martínez
Grupo de Biotecnologia Molecular
Instituto de Física de São Carlos
Universidade de São Paulo
http://limes.ifsc.usp.br/leandro
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