From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Wed Jun 22 2005 - 00:58:48 CDT
Thanks to everyone for their comments today concerning the water models.
This was something I have been thinking about and worried about. I had
sent an email to the mailing list previously (1-2 weeks ago) (which did
not get a response :() I also have remaining questions:
1) Are only 3 point models usable in NAMD? Can TIP4P or TIP5P even be
used in NAMD's current version?
2) How does "rigidBonds water" know that "water" is "water" in the .pdf
and .pdb files?
3) If a 4 point model is used, would SHAKE and RATTLE have to be used
explicitly to make the bonds and angles rigid (ie., "rigidBonds water"
would only work with a 3 point model ???)?
These may be elementary questions, I have only been using NAMD for ~1
month. Although there are many other comments in the mailing list
concerning water and rigidBonds, I cannot find the "explicit" answers to
these questions. Any response would be appreciated. In fact, I beg for a
Thanks in advance.
> 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
>> 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
>> the TIP3P model; however, this has been achieved by overestimating the
>> water-dimer interaction energy (i.e., the solvent-solvent interactions
>> too favorable). Although this overestimation is justifiable considering
>> omission of explicit electronic polarizability from the force field, it
>> cause problems when trying to produce a balanced force field due to the
>> 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. I
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