[gmx-users] charged proteins
David L. Bostick
dbostick at physics.unc.edu
Thu Mar 7 17:05:51 CET 2002
It's always a good idea to use ewald/PME for your simulation unless you
only want the intrinsic energy of a single molecule in energy minimization
(i.e. for force field development) or for some reason you don't want
periodicity. However if you wish to simulate say something like bulk water
or protein in bulk water, then you must use a box of water treated with
periodic boundaries. In these cases it is important to have a method to
treat long range coulomb forces beyond the coulomb cut-off unless you can
argue otherwise. There are some who argue that it is okay to treat systems
with a net charge with PME/ewald because the method introduces a so called
"positive background" charge effect. This tidbit varies depending on who
you ask... I have yet to prove it to myself that this is true.
David Bostick Office: 262 Venable Hall
Dept. of Physics and Astronomy Phone: (919)962-0165
Program in Molecular and Cellular Biophysics
CB #3255 Phillips Hall dbostick at physics.unc.edu
Chapel Hill, NC 27599 http://www.unc.edu/~dbostick
On Thu, 7 Mar 2002, Alan Wilter Sousa da Silva wrote:
> I believe there would have a polarization with charged protein specially
> using periodic boundary conditions (I'd like hear more here). However,
> and here goes my question, should not 'cut-off' avoid this problem? And
> with no charged protein, should I use PME? If so, for better results I'd
> have to use 'double-precison', wouldn't I?
> On Thu, 7 Mar 2002, David van der Spoel wrote:
> > On Thu, 7 Mar 2002, jozef hritz wrote:
> > > Dear Jocelyne,
> > >my oppinion is that for reliable simulation You have add to system
> > >counterions to charged aminoacids. Whole system should be electroneutral.
> > Indeed, and use PME.
> > Groeten, David.
> > ________________________________________________________________________
> > Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
> > Husargatan 3, Box 576, 75123 Uppsala, Sweden
> > phone: 46 18 471 4205 fax: 46 18 511 755
> > spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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> Alan Wilter S. da Silva
> Laboratório de Física Biológica
> Instituto de Biofísica Carlos Chagas Filho
> Universidade do Brasil/UFRJ
> Rio de Janeiro, Brasil
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