[gmx-users] Problems with TIP4P

[David]

On Thu, 2003-01-23 at 21:36, Justin MacCallum wrote:
> 
> Hi,
> 
> has anyone been able to get TIP4P to work with OPLSAA. I've made all of
> the relevant changes to tip4pgmx.itp to make it work with OPLSAA. Grompp
> runs without errors, however when I actually run the simulation the box
> blows up, and the Colomb energy (both LR and SR) is zero! I'm using
> 0.9/1.4 twin-range cutoffs. Any ideas?

I've attached mine which works fine. (Just submitted some 50 ns
simulations). This version is different in the sense that the order of
atoms is flipped (Mw-Hw1-Hw2-Ow). It gives considerably better
performance (by optimizing for quirks in gromacs innerloops).
A short optimzation/equilibration of your starting coords should do for
flipping the two atoms, as their original positions are quite close.

Don't expect better results than gromos though...

-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-------------- next part --------------
[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
1               2               yes             0.5     0.5


[ atomtypes ]
;name        mass      charge   ptype            c6           c12
   OW    15.99940       0.000       A   3.15365e-01   6.4852e-01
   HW     1.00800       0.000       A   0.00000E+00   0.00000E+00
   MW     0.000         0.000       D   0.00000E+00   0.00000E+00

[ moleculetype ]
; molname       nrexcl
SOL             1

#define MNO
#ifdef MNO
; We use a strange order of the atoms, this makes it considerably
; faster in GROMACS.
[ atoms ]
; id    at type res nr  residu name     at name         cg nr   charge
1       MW        1       SOL             DW              1       -1.04
2       HW        1       SOL             HW2             1       0.52
3       HW        1       SOL             HW3             1       0.52
4       OW        1       SOL             OW1             1       0

[ constraints ]
; i     j	funct   distance
2       4       1	0.09572 
3       4       1	0.09572 
2	3	1	0.15139

; The position of the dummy is computed as follows:
;
;               O
;
;               D
;
;       H               H
;
; const = distance (OD) / [ cos (angle(DOH))    * distance (OH) ]
;         0.015 nm      / [ cos (52.26 deg)     * 0.09572 nm    ]
;
; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-x1)

[ dummies3 ]
; Dummy from                    funct   a               b
1       4       2       3       1       0.128012065     0.128012065

[ exclusions ]
1       2       3       4
2       1       3       4
3       1       2       4
4       1       2       3

#else

[ atoms ]
; id    at type res nr  residu name     at name         cg nr   charge
1       OW        1       SOL             OW1             1       0
2       HW        1       SOL             HW2             1       0.52
3       HW        1       SOL             HW3             1       0.52
4       MW        1       SOL             DW              1       -1.04

[ settles ]
; i     funct   doh     dhh
1       1       0.09572 0.15139

; The position of the dummy is computed as follows:
;
;               O
;
;               D
;
;       H               H
;
; const = distance (OD) / [ cos (angle(DOH))    * distance (OH) ]
;         0.015 nm      / [ cos (52.26 deg)     * 0.09572 nm    ]
;
; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-x1)

[ dummies3 ]
; Dummy from                    funct   a               b
4       1       2       3       1       0.128012065     0.128012065

[ exclusions ]
1       2       3       4
2       1       3       4
3       1       2       4
4       1       2       3
#endif