From: Boonstra, S. (s.boonstra_at_rug.nl)
Date: Wed Apr 19 2017 - 05:20:31 CDT
Note that the protein parameters for CHARMM36 were partly parametrized
using standard TIP3P (Best, JCTC, 2012 - http://dx.doi.org/10.1021/ct300400x
<https://dx.doi.org/10.1021%2Fct300400x>), so without the LJ interactions
on the hydrogens.
This results in higher folded fractions of peptides with respect to the
CHARMM TIP3P water model (Boonstra, JPCB, 2016 -
The latest version of CHARMM, CHARMM36m (Huang, Nature Methods, 2016 -
http://dx.doi.org/10.1038/nmeth.4067), corrects for this by adjusting the
LJ well-depth of the water hydrogen atoms, although this is not a general
fix that works for all intrinsically disordered proteins.
Bottom line -- always use the water model that was used in the force field
parametrization that fits your system of interest, unless you have a valid
(physical) reason not to.
On Tue, Apr 18, 2017 at 11:56 PM, Brian Radak <bradak_at_anl.gov> wrote:
> Most NAMD users make use of the latest CHARMM force field (currently C36).
> These force fields have always, to my knowledge, been parameterized with
> the modified TIP3P potential which adds Lennard-Jones centers to the
> hydrogen atoms. This is not the same thing as TIP3P, although some reports
> in the literature equate the two. The standard TIP4P and TIP5P potentials
> are not widely used in biomolecular simulations. Some users occasionally
> use the TIP4P-Ew re-parameterization (usually with the AMBER force field).
> Ultimately the choice of solvent model is independent of NAMD - it can
> generally handle all of them. It all depends on what force field
> combination you think is most useful.
> On 04/18/2017 04:05 PM, Oscar Bastidas wrote:
> Would someone please tell me if TIP3P water molecules are the standard
> solvation for the version of NAMD presently available? I've heard of
> so-called TIP4P and TIP5P but I wasn't sure if these were special solvation
> models. Thank you.
> Respectfully submitted,
> Oscar B.
> Oscar Bastidas, Graduate Student
> Department of Chemical and Life Science Engineering
> Virginia Commonwealth University
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
> 9700 South Cass Avenue, Bldg. 240
> Argonne, IL 60439-4854
> (630) 252-8643
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