On Tue, 30 Jan 2007, David van der Spoel wrote:
Mark Abraham wrote:
Florian Haberl wrote:
1) how can i explaine "pH" into my system ( consisting protein & Na+
ions
) under gromacs? i'd like to reach to pH ~ 4.5 or 5 in my system.
What concentration of H+ ions are needed to get to these pH values? Can you
do that in a system with 10^4 to 10^5 atoms? Even if you can, there are no
MD water models that allow hydrogen atoms to dissociate freely, as happens
in real water.
This is not entirely correct, there are constant pH simulation models,
developed by Charlie Brooks and others where you can simulate transfer of
protons from one side chain to another. THis is not exactly what you need
here, and they only work in implicit solvent so far (and in Charmm at that).
I'd like to have such models implemented in gromacs, and with explicit
solvent. Anyone interested?
There are actually several constant-pH MD methods, some of them using
explicit solvent. We have ourselves developed a constant-pH MD method
based on stochastic protonation changes [J. Chem. Phys. (2002) 117:4184].
Although the method uses a Poisson-Boltzmann method to periodically change
the protonation states, the MM/MD simulations are done with explicit
solvent.
We have actually implementated this stochastic constant-pH MD method using
Gromacs [J. Phys. Chem. B (2006) 110:2927], basically following a
stop-and-go approach using bash and awk scripts to interface Gromacs with
MEAD (a PB solver by Don Bashford) and MCRP (a in-house program for Monte
Carlo sampling of protonation states). Unfortunately, the whole thing is
still too messy and hard-wired at some places, which makes it unsuitable
to be submitted as a contribution to Gromacs, at least for now.
Another explicit-solvent method, based only on MM/MD, was proposed by
Hunenberger [J. Chem. Phys. (2001) 114:9706], but its theoretical basis
seems to be wrong [J. Chem. Phys. (2002) 116:7766]. As far as I know, all
other constant-pH MD methods proposed so far used indeed implicit solvent.
Stochastic approaches using implicit solvent were used by McCammon [J.
Comput. Chem. (2004) 25:2038] and by Antosiewicz [Phys. Rev. E (2002)
66:051911], and we have also proposed a fractional-charge approach
[Proteins (1997) 27:523] where implicit solvent was used for computational
speed; all these methods depend on some sort of simplified
electrostatics-oriented method (Poisson-Boltzmann, generalized Born, etc)
to perform the protonation calculations. Implicit solvent was also used in
a method proposed by Brooks [Proteins (2004) 56:738], following a
different but theoretically vague approach to include protonation effects.
Antonio
--
Antonio M. Baptista
Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa
Av. da Republica, EAN, ITQB II, Apartado 127
2781-901 Oeiras, Portugal
phone: +351-214469619 email: [EMAIL PROTECTED]
fax: +351-214411277 WWW: http://www.itqb.unl.pt/~baptista
--------------------------------------------------------------------------
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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--
Antonio M. Baptista
Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa
Av. da Republica, EAN, ITQB II, Apartado 127
2781-901 Oeiras, Portugal
phone: +351-214469619 email: [EMAIL PROTECTED]
fax: +351-214411277 WWW: http://www.itqb.unl.pt/~baptista
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