[gmx-users] Using the CHARMM TIP3P water model in Gromacs

Nicolas SAPAY nsapay at ucalgary.ca
Wed Oct 11 01:18:12 CEST 2006

Hello all gmx users,

I'm doing some tests on the CHARMM TIP3P water model. After a several
consultations of the GROMACS mailing-list and doc, I still have some
First of all, I have used a tip3p.itp file were the TIP3 rigid water model
is defined :

[ moleculetype ]
;name   nrexcl
 TIP3   1
[ atoms ]
;id   atom_type   res     residu_name   atom_name      charge_group     
 1    OT          1       TIP3          OH2            1                
 2    HT          1       TIP3          H1             1                
 3    HT          1       TIP3          H2             1                

[ settles ]
; the SETTLE ALGORITHM is an analytical solution of SHAKE specifically for
;oxygen   func   d(O,H)    d(H,H)
 1        1      0.09572   0.15139

[ exclusions ]
; for non bonded interactions exclusion
1       2       3
2       1       3
3       1       2

Then, I have defined a TIP3 in a ffcharmm.rtp
[ TIP3 ]
[ atoms ]
;name    type       charge  charge_group
 OH2     OT        -0.8340             1
 H1      HT        +0.4170             1
 H2      HT        +0.4170             1

And finally, I have defined the LJ parameters in th ffcharmmnb.itp
HT         1.0080   0.000      A  3.153970e-09  1.292128e-17
OT        15.9994   0.000      A  2.489540e-03  2.434767e-06

This parameters are consistent with the implementation of Mark Abraham.
Everything works fine when I build the .top topology with pdb2gmxfile
except that the TIP3 residues in my pdb are not recognized as water and
are thus listed in the [atoms] section (the tip3p.itp is included by an
 command). I can fix that by creating a HOH or a SOL residue with same
property than TIP3  but I'm not sure it is a good idea. As far as I have
understood, GROMACS uses some specific code to improve the non-bonded
interactions computation of water. This code is designed for water models
without LJ parameters and I don't want to use it (since TIP3P has got LJ
paramters in CHARMM). But in this case, I not sure that my TIP3 residues
will be considered as rigid water model and then that the H1...H2
distance will be constrained (I don't use the -DFLEXIBLE flag in my .mdp
file and use the -I flag ot include the directory where the CHARMM force
field is defined).

So, is my use of the TIP3P model correct with GROMACS?

Thanks for your comments!


[ Nicolas Sapay Ph.D. ]
University of Calgary, Dept. of Biological Sciences
2500 University Dr. NW, Calgary AB, T2N 1N4, Canada
Tel: (403) 220-6869
Fax: (403) 289-9311

More information about the gromacs.org_gmx-users mailing list