[gmx-users] Settle vs. 3 normal constraints

[Andreas Mecklenfeld]

Dear GROMACS users,

I want to calculate the solvation free energy of a rigid water molecule, 
e.g. TIP4P-Ew.
To do this, I define one solute molecule which I refer to as 
couple-moltype in the .mdp-file (SOL).
The solvens molecules are exactly the same, just named differently for 
distinction (SOLB).

Since I can't simulate two molecule types with settle, I want to use 
constraints. My .itp-file looks like this:

----------------------------------------------------------------------------------------------------

;
; tip4pew Water model
;
[ moleculetype ]
; molname    nrexcl
SOL        2

[ atoms ]
; id  at type     res nr  res name  at name  cg nr  charge    mass
   1   OW_tip4pew  1       SOL       OW       1       0 16.00000
   2   HW_tip4pew  1       SOL       HW1      1       0.52422 1.00800
   3   HW_tip4pew  1       SOL       HW2      1       0.52422 1.00800
   4   MW                1       SOL       MW       1      -1.04844 0.00000



[ constraints ]
1    2    1    0.09572    ; func. 1: chemical bond (O-H)
1    3    1    0.09572    ; func. 1: chemical bond (O-H)
2    3    2    0.15139    ; func. 2: no chemical bond (H-H)



[ virtual_sites3 ]
; Vsite  from              funct   a               b
4       1       2       3       1       0.106676721     0.106676721


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


; The position of the virtual site is computed as follows:
;
;          O
;
;          V
;
;    H        H
;
; Ewald tip4p:
; const = distance (OV) / [ cos (angle(VOH))     * distance (OH) ]
;      0.0125 nm    / [ cos (52.26 deg)    * 0.09572 nm    ]
;    then a = b = 0.5 * const = 0.106676721
;
; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1)

----------------------------------------------------------------------------------------------------

The temperature derivates by 20 K using the sd-intergrator as thermostat.
By using the settle algorithm for only one molecule (same .mdp and .gro
files as for the constrained), I gain results as expected.

I'm sorry if this is a trivial question.

Thanks for your support!
Andreas


-- 
M. Sc. Andreas Mecklenfeld
Stipendiat

Technische Universität Braunschweig
Institut für Thermodynamik
Hans-Sommer-Straße 5
38106 Braunschweig
Deutschland / Germany

Tel: +49 (0)531 391-2634
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