[gmx-users] C6 & C12 parameters for non-bonded interactions using tables
mark.j.abraham at gmail.com
Wed May 22 16:30:12 CEST 2013
Exactly a factor of ten? Angstrom vs nm issue?
On Wed, May 22, 2013 at 4:09 PM, Andrish Reddy <areddy at csir.co.za> wrote:
> 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
> 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
> 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
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