[gmx-developers] Re: gmx-developers Digest, Vol 32, Issue 4

Qiao Baofu qiaobf at gmail.com
Mon Dec 11 13:49:40 CET 2006

Hi David,

Thanks for your kindly reply. I use the gmxdump to check the LJ-14 term in
the test.tpr file, but find the it only lists the pairs, and the scaled
parameters are not there. Can you tell me how to check the effect of the
scaling factor?  Thanks

I use the combin-rule =2, not the default value 3 of ffoplsaa. But I don't
know what is wrong with it. Can you explait it clearer? Thanks!

This morning, I did another set of tests:
I use the ffoplsaa force field. In the .itp file, I write the LJ-14
interaction parameter by hand, and scaled epsilon_{ij} by 0.5. In the
ffoplsaa.itp file, I used
 ; nbfunc     comb-rule    gen-pairs    fudgeLJ   fudgeQQ
    1              2                no              n       0.8333
I set n=1, 0.5, 0.25, 0.1. Then mdrun. But I get different LJ-14 energy in
the .log file.

1.  fudgeLJ =1                  LJ-14= 2.25122e+02
2.  fudgeLJ =0.5               LJ-14=1.53262e+02
3. fudgeLJ =0.25              LJ-14=1.19950e+02
4. fudgeLJ =0.1                LJ-14= 1.04176e+02

It is strange, even though I used genpairs =no, when I change the value of
fudgeLJ, the LJ-14 energy change with the value (not linear!!)

> Message: 1
> for the effect of the scaling factor you should compare the tpr files.
> the problem might also be that you have the wrong combination rule: 2 iso
> 3.
> --
> David.
> _______________________________________________________________________
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