From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue Sep 29 2015 - 13:25:07 CDT
Hi Shayon,
>From what I've always seen, the effects of the hydrogen vdw site is
basically non-existent because of how small it is relative to the oxygen,
as you note. It was also shown in
http://pubs.acs.org/doi/abs/10.1021/ct900549r that the hydrogen vdw
parameter makes almost no difference. In all of my TIP4 files I used the
original TIP4 definition of no hydrogen vdW site (which is what you get
with epsilon=0); the comments in that tip4p.par file that you link to are
somewhat misleading in that respect (oops). I don't know what Jordi
Faraudo's logic is for having hydrogen vdw sites there; people put the
hydrogen vdw site on charmm style tip3 water (TIPS3P), but I am not aware
of anyone advocating that for any of the TIP4 models.
>From my understanding the safest recommendation is to use the TIPS3P model
with charmm force fields (that is what they were parameterized with) even
though TIP3P is virtually equivalent (and might be preferred for
performance reasons). Things get dicey very fast if you try using ANY TIP4
models with charmm forcefields, because of how deeply the water model is
baked into the charmm parameterization procedure. People do it, sometimes
it seems to work well, but there's no reason to expect that it actually
SHOULD give reasonable results. So I think the best advice there is (1)
think three times about whether that's really a good idea, and (2) if you
do, the water hydrogen vdw parameters are probably the least of your
problems, but if MacKerell's group has them turned off in his TIP4 files,
that's probably the place to be.
Best,
Peter
On Tue, Sep 29, 2015 at 11:20 AM, Shayon Bhattacharya <
shayon.bhattacharya_at_gmail.com> wrote:
> Dear NAMD list,
>
> I am running simulations with various TIP4P water models (TIP4P, TIP4P-Ew,
> TIP4P/2005, etc) for my protein to test a certain feature and choose the
> right model for my simulation - all using CHARMM36 FF for proteins. I have
> used the tip4p kit from Peter -
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2011-2012/0322.html
> with the pre-equilibrated water box, and also using this for the other
> water models (generating psfs of boxes with different topologies).
>
> I see that the Mackerell website have these tip4p water model parameters
> (in toppar stream files) with no values (they are zeroes) on the Hydrogen
> Lennard-Jonnes parameters - epsilon and Rmin/2 as used in charmm
> convention, whereas the parameter file from Peter has a Rmin/2 value of
> 0.0250, while the epsilon is 0. Same applies for tip4p/2005, where the
> parameter file from Jordi Faraudo has hydrogen LJ values of -0.046 and
> 0.2245 respectively for epsilon and Rmin/2, whereas the one from Mackerell
> website had zeroes in place.
>
> Knowing that the oxygen LJ parameters are what matters, and the vdw radii
> for oxygen is bigger than hydrogen, my question is do the LJ parameters for
> hydrogen really matter? If so, why such discrepancies in values for NAMD
> compatible Charmm conventions?
>
> thank you,
> Shayon
> --
> Shayon Bhattacharya
> PhD student
> Department of Physics and Energy
> University of Limerick, Ireland
>
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