[gmx-users] C6 & C12 parameters for non-bonded interactions using tables

Andrish Reddy areddy at csir.co.za
Wed May 22 16:09:36 CEST 2013


I am trying to use tabulated potentials for the VdW interactions between
TIP5P water molecules.
I have tested my topology file to make sure that it gives reasonable results
with the standard table6-12.xvg in the /top folder and C6=4*eps*sig^6 ,
C12=4*eps*sig^12.  I am able to match the energies with an identical run not
using look-up tables. The problem comes when I want to include the C6 & C12
parameters within the table. This is needed for dealing with more complex
multi-parameter potential functions. 

I tried testing this with the standard Lennard-Jones potential. Setting
g(r)=-(4*eps*sig^6)/r^6 and h(r)=(4*eps*sig^12)/r^12. I then construct my
table according to [r,f(r),-f'(r),g(r),-g'(r),h(r),-h'(r)]

I set vdw-type = user in my mdp file and modified my topology so that:
[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
1               1               yes             0.5     0.8333

[ atomtypes ]
; name      at.num  mass     charge ptype  C6      C12
OW_tip5p     8      16.00    0.0000  A   1.00000e+00  1.00000e+00

Since C6 & C12 = 1, this run should be identical to using the table6-12.xvg
and C6=4*eps*sig^6 , C12=4*eps*sig^12
The run proceeds fine with no warnings or errors, but the LJ and Potential
energies are an order of magnitude higher than when using the standard
table. I don't understand why I am not able to reproduce the results by this


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