Hi,
thank you for your comments and explanation, now I understand it. Hopefully
I will finish the simulation successfully.
On Thu, May 26, 2011 at 9:28 AM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> > Yes, there is some problem with the system "stability", therefore I was
> > trying to fix the system by restraints. Also in such case I saw
> unexpected
> > geometry changes. I have checked the toplogy, it seems to be all right to
> > me.
>
> if your system extends beyond the virtual box, you should see it moving
> around a lot when you view the trajectory, unless it is something like a
> really wound up thread that unfolds. Again, that is something you should
> see.
>
> Yes, there is problem in coordinates, but I cant find the source of the
error. Anyway, I would prefer usage of newest Amber version without ifsc=2
option as it was discussed below.
> > with the change of deltaG. In following step - atoms disappearing, the
> non
> > bonded interactions are removed. I would again expect the change of
> > deltaG.
>
> that depends on your definition of disappearing. In Amber11, that is
> 'removing all interactions between disappearing atoms and their
> non-disappearing surroundings, while keeping intermolecular interactions
> intact'. Therefore, the disappearing in vacuum leg of your cycle does not
> really change anything and deltaG is zero.
>
> > with the complete perturbation. I am just wondering if the zero value for
> > deltaG is an reasonable approximation for larger molecules.
>
> It is not an approximation, nor connected to system size. The point is
> just where to put the zero point of energy, which is arbitrary and does
> not influence your final result.
>
I understand, thanks.
Kind Regards, Zora
>
> Kind Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
==========================================
Zora Strelcova
==========================================
National Centre for Biomolecular Research (NCBR)
Faculty of Science, Masaryk University
Kotlarska 2, 611 37 Brno, Czech Republic
=========================================
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Received on Thu May 26 2011 - 01:00:02 PDT
