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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Received on Wed Jul 27 2011 - 10:00:02 PDT
