From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Jun 21 2005 - 17:40:15 CDT
So my question remains. How was the tip4p and tip5p parameterized? Which
protein force field was used? Charm22, Charm27 charmXX? The tip5p is a
radically different beast than tip3p. I would say there is more
difference between tip5p and tip3p than between tip3p and f3, but that
could be argued.
So if the water model changed so dramatically what is happening to the
protein side of the force field? All I am doing is testing the protein
side of the charmm FF against a different water model, in the same way as
people have done for tip5p. And so far the protein dynamics are not
different from what I have seen before using ENCAD and F3C. One caveat, I
don't have access to encad anymore for realtime head to head
On Tue, 21 Jun 2005, Blake Charlebois wrote:
> Here is a quote from Alexander D. MacKerell (the PI in charge of the CHARMM
> force field, if I am not mistaken) from page 22 of A.D. MacKerell Jr.,
> "Atomistic Models and Force Fields," in Computational biochemistry and
> biophysics, O.M. Becker Ed. 2001, pp. 7-38.
> "The SPC/E water model is known to yield better pure solvent properties than
> the TIP3P model; however, this has been achieved by overestimating the
> water-dimer interaction energy (i.e., the solvent-solvent interactions are
> too favorable). Although this overestimation is justifiable considering the
> omission of explicit electronic polarizability from the force field, it will
> cause problems when trying to produce a balanced force field due to the need
> to overestimate the solute-solvent and solute-solute interaction energies in
> a compensatory fashion. Owing to this limitation, the TIP3P model is
> suggested to be a better choice for the development of a balanced force
> field. It is expected that water models that include electronic polarization
> will allow for better pure solvent properties while having the proper
> solvent-solvent interactions to allow for the development of balanced force
> fields. It is important when applying a force field to use the water model
> for which that particular force field was developed and tested. Furthermore,
> extensions of the selected force field must maintain compatibility with the
> originally selected water model."
> I interpret this to mean that changing the water model is dangerous unless
> you really know what you are doing.
> -----Original Message-----
> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
> Of Marc Q. Ma
> Sent: June 21, 2005 3:12 PM
> To: Leonardo Sepulveda Durán
> Cc: oakley_at_rsc.anu.edu.au; namd-l
> Subject: Re: namd-l: Solvent model other than TIP3 for use with CHARMM FF in
> Dear all,
> My understanding was that TIP3P rigid water model is just one of many
> existing force fields for liquid water. FF for liquid water is
> independent of any FF for proteins and DNAs and lipids and ... It just
> happened that TIP3P is the most popular one to go with CHARMM for
> solvated biomolecule simulations. And, probably a preference, a
> shortcut, or a "mistake" by NAMD developers not to leave water models
> as a choice. For example, when you specify rigid waters, NAMD assumes
> TIP3P model automatically and apply SHAKE or RATTLE iterations to make
> the 3 point water molecules rigid.
> Computing self diffusion coefficients can be very tricky in using any
> FF for liquid water. You got to use block averaging, and weather you
> choose overlapping or non-overlapping blocks, block sizes, and the
> region that you "think" is the "true" linear region according to
> Einstein's equation all contribute to the accuracy/inaccuracy of
> computation of this "observable." Arguably true, if you use small time
> steps such as 1fs, and keep all long range forces, you should get the
> best estimates of self diffusion coefficient as long as you run long
> enough simulations, or use hybrid Monte Carlo to improve the sampling
> efficiency and egodicity of simulations.
> My experience with computing RDF for TIP3P water model is that the
> peaks and valleys are all clearly shown, and the 1st and 2nd peaks (1.9
> aa and 3.3 aa) for O-H RDF indicate the 1st and 2nd strongest H-bond
> distance. From the same 400ps simulations, the self diff coeff is
> estimated to be 3.69+/0.01 (10^-5 cm^2 s) for 300 K temperature. I
> believe the experimental value is around 2.5.
> I hope one day NAMD would have full support of many different water
> models, including the various implicit solvent models. That will leave
> serious developers lots of option to do verification and discovery.
> Right now, researchers have to go from software to software to take
> advantage of the best features of each one.
> On Jun 21, 2005, at 1:42 PM, Leonardo Sepulveda Durán wrote:
> > Yesterday I read the 1997 F3C Levitt's paper. In table 3 a comparison
> > to other published 3 point models. TIP3P is far one of the worst
> > models, it have a Diffusion coefficient double than experimental, and
> > the rdf don't show the two long range peaks, suggesting the lack of
> > water tetrahedral structure. In the other hand, SPC/E (or even SPC)
> > shows features very similar to F3C.
> > In the paper they argue consitency in molecular representation is an
> > important issue, so if Angle and bond degrees of freedom are allowed
> > in solute, it must be in water too. So as CHARMM and ENCAD have fairly
> > the same type of armonic potentials, and in F3C parametrization the
> > only ENCAD related issues they use were different cutoff methods, F3C
> > would be independent of ForceField and its implementation would depend
> > on cutoff or algoritmic issues (as long as the FF would be like AMBER,
> > CHARMM or ENCAD).
> > If CHARMM forcefield was parametrized with TIP3P and that is important
> > to the solute parameters, then may be some problems...but I hope
> > Brian's research could succeesfully solve them to have a broader
> > variety of solvents for NAMD/CHARMM use.
> > Leonardo
Brian Bennion, Ph.D.
Lawrence Livermore National Laboratory
P.O. Box 808, L-448 bennion1_at_llnl.gov
7000 East Avenue phone: (925) 422-5722
Livermore, CA 94550 fax: (925) 424-6605
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