[gmx-users] TIP5P and Free Energy

[Ronen Zangi]

Dear All,

I have a problem that somebody may had encountered and solved. Running TIP5P 
with the Free energy option in the mdp file seems to go wrong (density is 
getting lower and lower). This occurs with all versions that I checked 
3.2.1,  3.1.4 and 3.0.5.

Running TIP5P without Free Energy is good. Running SPC (for exmaple) with 
Free Energy is also good. I would guess that it is becuase of the 
combination of the
[ dummies3 ] entery in the top file of TIP5P and the Free Energy option.

Below is the top file that I use (it didn't help to change the combination 
rule to 3 with sigma and epsilon instead of c6 and c12).

Any help would be appreciated,

Ronen





[ defaults ]
nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
  1                 1                         no              1.0            
1.0

[ atomtypes ]
;name   mass      charge   ptype       c6         c12
OW     15.99940   0.000       A   0.00247001   2.27838e-06
HW      1.00800    0.241        A     0.0          0.0
OL       0.0           -0.241        D     0.0          0.0
LJP    40.0           0.000         A    0.0625    0.000976562



[ moleculetype ]
; Name            nrexcl
LJG                 1

[ atoms ]
;nr  type  resnr residue  atom   cgnr  charge  mass
1    LJP     1        LJG       LJ1     1       0.0       40.0
2    LJP     1        LJG       LJ2     1       0.0       40.0

[ constraints ]
; #at.   f.tp  length_A  Length_B
1  2       2     0.440     1.440


[ moleculetype ]
; molname       nrexcl
SOL               2

[ atoms ]
; id    at type res nr  residu name     at name         cg nr   charge
1       OW      1       SOL              OW             1       0
2       HW      1       SOL             HW1             1       0.241
3       HW      1       SOL             HW2             1       0.241
4       OL      1       SOL             OL1             1      -0.241
5       OL      1       SOL             OL2             1      -0.241

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

[ dummies3 ]
; The position of the dummy is computed as follows:
;
; The distance from OW to OL is 0.07 nm, the geometry is tetrahedral
; (109.47 deg)
; Therefore, a =3D b =3D 0.07 * cos (109.47/2) / | xOH1 + xOH2 |
;            c =3D 0.07 * sin (109.47/2) / | xOH1 X xOH2 |
;           =20
;
; Using | xOH1 X xOH2 | =3D | xOH1 | | xOH2 | sin (H1-O-H2)
;       | xOH1 + xOH2 | =3D 2 | xOH1 | cos (H1-O-H2)
; Dummy pos x4 =3D x1 + a*x21 + b*x31 + c*(x21 X x31)

; Dummy from                    funct   a       b               c
4       1       2       3       4       -0.344908  -0.344908  -6.4437903493
5       1       2       3       4       -0.344908  -0.344908   6.4437903493

[ exclusions ]
1       2       3       4       5
2       1       3       4       5
3       1       2       4       5
4       1       2       3       5
5       1       2       3       4



[ system ]
; Name
LJG SOL

[ molecules ]
; Compound        #mols
LJG                1
SOL               1198

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