I don't know about GROMACS but, as I said, the numbers in the last two
columns are the numbers that need go to the "AMBER" topology files. If you
used numbers in the columns of 'A' and 'B', your numbers were wrong.
2011/7/27 Bongkeun Kim <bkim.chem.ucsb.edu>
> Yes, I used that equation for comparison with gromacs.
> Bongkeun Kim
>
> Quoting InSuk Joung <i.joung.gmail.com>:
>
> > 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
> >> >
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> 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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>
--
Best,
InSuk Joung
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Received on Wed Jul 27 2011 - 13:00:42 PDT
