[AMBER] Changing the L-J parameter does not work?

From: <bkim.chem.ucsb.edu>
Date: Wed, 27 Jul 2011 09:58:41 -0700

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