[gmx-developers] flexible water model

[Nilesh Dhumal]

Hello,

I am using flexible water model for my system. I am referring a paper J.
Chem. Phys. 124, 024503 (2006). Author have used Amber type force field.

i.e. 1/2 Kbond (r-req)**2 + 1/2 Kangle(theta-thetaeq)**2.

Kbond = 443153.3808 kJ/mol nm**2

Kangle= 317.5656 kJ/mol rad**2.

I am using olss-aa force field parameters in Gromacs  VERSION 4.0.7.

I checked some papers in which author have used oplsaa force field in
Gromacs. 1/2 factor is not in opls force field if I compare opls and
amber.


I didn’t get the proper dielectric constant for water when I used the
parameters reported in paper

(Kbond = 443153.3808 kJ/mol nm**2,Kangle= 317.5656 kJ/mol rad**2)

 I half the value of Kb and get the proper dielectric constant (~80) for
water reported in paper. If I half Kangle  then I don’t get proper
value.
Below are the results for the dielectric constant of water.
Bond length is nm.

Here I have done some analysis.  The original value reported in J. Chem.
Phys. 124, 024503 2006, paper are

Kbond = 443153.3808 kJ/mol nm**2
Kangle = 317.5656 kJ/mol rad**2.


 bond length    Kbond       angle    Kangle    dielectric constant  0.1012
      443153.3808    113.24  317.5656       ~1.9 : orginal value


 0.1012       221576.6904    113.24  317.5656       ~80   : 1/2 (Kbond)


 0.1012       443153.3808    113.24  158.7828       ~1.58 : 1/2 (kangle)


 0.1012      221576.6904    113.24  317.5656       ~1.9   : 1/2
 (Kbond)&(Kangle)


Here I pasted spc_fw.itp file used for the simulation.

; Derived from parsing of runfiles/alat.top.orig
 [ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
;1               3               yes             0.5     0.5
; comb-rule 3 is square-root sigma, the OPLSAA version

 [ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name  bond_type    mass    charge   ptype          sigma      epsilon
 opls_1001  OW  8     15.99940    -0.820       A    3.1655e-01   6.503e-01
 opls_1002  HW  1      1.00800     0.410       A    0.00e+00     0.00e+00

[ bondtypes ]
; i    j  func       b0          kb
  OW    HW      1    0.1012   443153.3808   ; J. Chem. Phys.
(2006),124,024503
[ angletypes ]
;  i    j    k  func       th0       cth
  HW     OW     HW      1   113.24  317.5656 ; J. Chem. Phys.
(2006),124,024503

[ moleculetype ]
; Name            nrexcl
 WAT             3

[ atoms ]
; nr       type  resnr residue  atom   cgnr     charge       mass  typeB
 chargeB      massB
     1   opls_1001     1    WAT     OW      1      -0.82     15.99940 ;
     2   opls_1002     1    WAT    HW1      1       0.41      1.008   ;
     3   opls_1002     1    WAT    HW2      1       0.41      1.008   ;

[ bonds ]
; i     j       funct
    1     2     1
    1     3     1

[ angles ]
; i     j       k       funct
   2     1     3     1

In water.top file, I included spc_fw.itp file.

; Include water topology
#include "spc_fw.itp"


I run the simulation 6.5 ns for collecting data and I have total 256
water molecules.


Is there anything wrong with my .itp file?

I am using Gromacs VERSION 4.0.7.



Thanks

Nilesh