[gmx-users] molecule order optimization?

[David van der Spoel]

On Tue, 2003-02-25 at 09:07, Michael Shirts wrote:
> 
> So, I'm running a box of tip4p waters, using the 3.1.4-included tip4pgmx.itp
> file.  I get the warning:
> 
> The order in molecule 0 could be optimized for better performance
> The order in molecule 1 could be optimized for better performance
> The order in molecule 2 could be optimized for better performance
> .
> .[and so forth]
> .
> (More than 10 molecules where the order can be optimized)
> 
> I've experimented changing the order in the .gro files, but that doesn't seem
> to do anything.  For four (and five) point solvent molecules, is there a "good
> order" that will optimize performance? If so, does one need to change the .itp
> file?  Or does this warning just pop up when using a non-three point water?
> 

I'm attaching an optimized tip4p topology. It will save you up to 30%
runtime.


-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. 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