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
>
>
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>
--
Best,
InSuk Joung
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Received on Wed Jul 27 2011 - 11:30:02 PDT
