[gmx-users] vdW parameters and atoms moving too fast

Mark Abraham Mark.Abraham at anu.edu.au
Wed Feb 7 04:15:38 CET 2007

Nicolas SAPAY wrote:
> good remark... here is the files! I precise that modifying the
> inter-atomic distance doesn't solve the problem and that nb parameters are
> defined in the ffcharm27nb.itp file as follow :
> [ atomtypes ]
> OT        15.9994   0.000      A  2.489540e-03  2.434767e-06
> HT         1.0080   0.000      A  3.153970e-09  1.292128e-17
> [ nonbond_params ]
> OT     HT      1     4.382447e-05  1.371950e-09

Well the good news is that my CHARMM27 implementation agrees with these 
C6 and C12 values... for reference, I use these with

[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
    1            1               yes             1.0     1.0

and see no problems.

> [ pairtypes ]
> OT     HT      1     4.382447e-05  1.371950e-09

This shouldn't be needed, but won't be causing problems.

I can't see anything wrong with your .top or .mdp files.

The V and W values in the [ atomtypes ] section won't be being used, 
because of the existence of this defined interaction in [ nonbond_params 
], so you can test that that's correct by zeroing these values and 
looking for no change in the output. They look wrong, though, and 
certainly don't combine using comb-rule 1 to give the correct values.


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