[gmx-users] Binary mixture

Abhishek Banerjee a.banerjee at ymail.com
Tue Sep 1 14:48:14 CEST 2009

Hi all,
                 Thanks a lot for your reply. Actually I will tell you the problem. I want a binary mixture of DMF and methanol. Then I want to study the self diffusion coefficient as function of mole fraction of ant of the component. Now I got a reference about DMF. They used CS2 model with six interaction sites of DMF. So I took all the parameters and wrote a separate itp file. 
#ifdef _FF_OPLS

[ atomtypes ]

;type    mass    charge       ptype          sigma          epsilon

 CH3     15.0350   0.280        A            3.80000e-01    8.00000e+01

  N      14.0067  -0.570        A            3.20000e-01    8.00000e+01

  C      12.0110   0.570        A            3.70000e-01    5.00000e+01

  O      15.9994  -0.500        A            2.96000e-01    1.00000e+02

  H       1.0008   0.060        A            2.20000e-01    8.00000e+00


[ moleculetype ]

; Name nrexcl

DMF      3

#ifdef _FF_OPLS

[ atoms ]

;   nr      type  resnr resid  atom  cgnr   charge

     1       CH3     1  DMF      C1     1    0.280

     2         N     1  DMF       N     1   -0.570

     3       CH3     1  DMF      C2     1    0.280

     4         C     1  DMF       C     1    0.570

     5         O     1  DMF       O     1   -0.500

     6         H     1  DMF       H     1    0.060


"dmf.itp" 42L, 1288C

Now my question is how do i make a solvent box of DMF with this itp file. Plz help

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