[gmx-users] Re: VDW switched off in CHARMM tip3p model

qiuxing wz24 at zips.uakron.edu
Thu Aug 15 01:06:00 CEST 2013

TIP3P and TIPS3P (which I found later is the CHARMM TIP3P) produce slightly
different water bulk density:
0.96 vs. 1.01 when using CHARMM ff set, but TIPS3P is almost two times
slower than original TIP3P. For the benefit of TIPS3P, I think it heavily
depends on applications.


Christopher Neale wrote
>>From my inspection of the force field files included in gromacs-4.6.1,
when you
> use the charmm ff and the charmm tip3p (tips3p.itp) you get the hydrogen
> type HT,
> which does have LJ on the hydrogen atoms, whereas you only get the
> hydrogen 
> type HWT3 when you use the non-charmm tip3p (tip3p.itp).
> If I understand Mark's comment to be that there is no good reason to use
> the charmm
> tip3p water model with the charmm ff, then I disagree (See below).
> I have posted an image ( http://tinypic.com/r/110ak5s/5 ) of the area per
> lipid (APL) 
> for a POPC bilayer that I built with charmm-gui (83 lipids/leaflet; 43
> waters/lipid)
> and then simulated under the charmm36 lipid parameters for ~ 300 ns many
> times 
> successively with different water models (2 repeats each, starting from
> different 
> conformations out of charmm-gui). Note the large difference in the APL for
> the 
> regular tip3p and the charmm tip3p.  In fact, some papers note that you
> get 
> gel-phase bilayers with the charmm36 lipid ff and the non-charmm tip3p
> model when using 
> certain cutoff treatments 
> (Piggot and Khalid -- http://pubs.acs.org/doi/abs/10.1021/ct3003157 -- is
> one such paper).
> Chris.
> -- original message --
> You could do that, but it's extra cost for no known benefit. See
> http://dx.doi.org/10.1021/ct900549r
> On Tue, Aug 13, 2013 at 7:15 PM, Weilong Zhao 
> <wz24 at zips.uakron.edu>
>  wrote:
>> Hi,
>> I noticed that for GROMACS versions of 4.5 of later, the force field for
>> TIP3P water model in CHARMM27.ff package has a following line included:
>>  The following atom types are NOT part of the CHARMM distribution
>> ..
>> .
>> HWT3    1       1.008000        0.417   A       0.0     0.0     ; TIP3p H
>> It seems that VDW interaction of the default hydrogen of water is
>> switched
>> off, which makes it not the correct TIP3P ff of CHARMM. However this
>> hydrogen type HWT3, is used as default by gromacs as CHARMM water model.
>> Even though the hydrogen without VDW is the original TIP3P water model, I
>> wonder is there any problem to include it in CHARMM ff set? Really
>> appreciate if anyone could share some opinion.
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