Hi,
thank you for the comments.
On Wed, May 25, 2011 at 4:10 PM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> > I would like to pertube system (7 residues) in vacuum to nothing, but I
> am
> > forcing several problems:
>
> what happens when you look at your system trajectory? If you have
> restraints on and the molecule still moves beyond the virtual box
> something strange is going on...
>
>
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.
> > On the other hand, I would like to run all TI simulations in amber 11.
> > Since ifsc=2 option is no more implemented in this version, I would like
>
> In Amber11 doing a full soft core transformation of a molecule to
> 'nothing' would amount to a deltaG of zero, hence ifsc=2 was removed as it
> is no longer necessary. In fact the transformation does not really
> 'remove' the molecule, it shifts it into a state not interacting with its
> environment, 'quasi vacuum'. Doing that starting in vacuum just means that
> nothing really changes. What kind of thermodynamic cycle would require the
> calculation that you describe?
>
>
I would like to calculate the solvation energy. My thermodynamic cycle is
build as it follows:
vacuum: System(charged) ----> system (discharged) ------> disappeared system
|
| |
solvent: System(charged) ----> system (discharged) ------> disappeared
system
I am not sure, if I understand your explanation well. In first step of the
cycle (discharging) I am removing electrostatics - this change is connected
with the change of deltaG. In following step - atoms disappearing, the non
bonded interactions are removed. I would again expect the change of deltaG.
Using such approach, I wont be able to estimate all the energies connected
with the complete perturbation. I am just wondering if the zero value for
deltaG is an reasonable approximation for larger molecules.
Kind regards, Zora
Kind Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> 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 Wed May 25 2011 - 13:00:03 PDT
