If your sigma is the one in the equation,
V(LJ) = 4 *epsilon ( (sigma/r)^12 - (sigma/r)^6 )
ACOEFF and BCOEFF in your table (last two columns) are the correct numbers
you need to put in the AMBER topology file.
2011/7/27 Bongkeun Kim <bkim.chem.ucsb.edu>
> I already checked the unit and the values of A and B Coeff.
> And this is my parameter setup both on amber and gromacs.
> --------------------------------
> ¥ò (Å) ¥å (kJ/mol) ¥å (kcal/mol) A B ACOEFF
> BCOEFF
> 3.2823 0.4839 0.1156 1.808E+05 2.892E+02 7.234E+05
> 5.784E+02
> 3.2823 0.3000 0.0717 1.121E+05 1.793E+02 4.485E+05
> 3.587E+02
> 3.2823 0.3500 0.0837 1.308E+05 2.092E+02 5.232E+05
> 4.184E+02
> 3.2823 0.4000 0.0956 1.495E+05 2.391E+02 5.980E+05
> 4.782E+02
> 3.2823 0.4500 0.1076 1.682E+05 2.690E+02 6.727E+05
> 5.380E+02
> 3.2823 0.5000 0.1195 1.869E+05 2.989E+02 7.475E+05
> 5.978E+02
> 3.2823 0.5500 0.1315 2.056E+05 3.288E+02 8.222E+05
> 6.575E+02
> --------------------------------------------------------
> Thanks.
> Bongkeun Kim
> bkim at chem.ucsb.edu
> Quoting InSuk Joung <i.joung.gmail.com>:
>
> > Hi,
> > As fas as I know, your way to modify the topology file is correct
> although
> > you should be careful as the system gets more complicated.
> >
> > I have some suggestions you can try. First, make sure that A and B
> > coefficients are calculated with units of Angstrom and kcal/mol (not
> > kJ/mol). You probably understand that you only tried to modify C-O
> > interactions not C-C interactions. Double-check if it is the same in your
> > GROMACS setup.
> >
> > On Wed, Jul 27, 2011 at 12:58 PM, <bkim.chem.ucsb.edu> wrote:
> >
> >> Hello,
> >>
> >> I am running a simulation which has only carbon atoms(graphite) and
> SPC/E
> >> water molecules to calculate the contact angle in NVT.
> >> I made the different sets of input files with different prmtop files in
> >> which the L-J parameter between carbons and oxygens.
> >>
> >> In each prmtop file, I have only 3 atom types (C, O and H) and the non
> >> bonded parm index is given as
> >> ---------------
> >> FLAG NONBONDED_PARM_INDEX
> >> %FORMAT(10I8)
> >> 1 2 4 2 3 -1 4 -1 6
> >> ----------------
> >>
> >> So the L-J parameter for C-O are in the second position in each A and B
> >> coeff.
> >> ----------
> >> %FLAG LENNARD_JONES_ACOEF
> >> %FORMAT(5E16.8)
> >> 8.19971662E+05 7.23869979E+05 6.29362166E+05 0.00000000E+00
> >> 0.00000000E+00
> >> 0.00000000E+00
> >> %FLAG LENNARD_JONES_BCOEF
> >> %FORMAT(5E16.8)
> >> 5.31102864E+02 5.78465890E+02 6.25267765E+02 0.00000000E+00
> >> 0.00000000E+00
> >> 0.00000000E+00
> >> %FLAG
> >> -------------------
> >>
> >> I changed the second coefficients from epsilon values varying from
> >> 0.3kJ/mol to 0.5kJ/mol and also from sigma values from 3.0A to 3.3A. I
> >> checked the amber FAQ to convert these values to the ones of r and
> epsilon
> >> and to 12-6 A and B coefficients.
> >>
> >> But I have currently no changes in contact angles from 14 different
> runs.
> >> The average WCA only changes +-1 degrees with different L-J parameters.
> >> But in my previous simulations in GROMACS which I modified sigma and
> >> epsilon values only on carbon atoms(there is no option to define pair
> >> parameter in topology file) can show about +-10 degree changes for total
> >> set of different parameters.
> >>
> >> Is there any other parameter that I need to change in the prmtop file?
> >> Thank you.
> >> Bongkeun Kim
> >> bkim at chem.ucsb.edu
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Best,
> > InSuk Joung
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Best,
InSuk Joung
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Received on Wed Jul 27 2011 - 13:00:30 PDT
