[gmx-developers] problem about fudgeQQ and fudgeLJ (maybe a bug)

[David van der Spoel]

Qiao Baofu wrote:
> I have posted the question using the <gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>>, but no reply. Therefore, I submit it here.
> 
> ---------- Forwarded message ----------
> From: *Qiao Baofu* <qiaobf at gmail.com <mailto:qiaobf at gmail.com>>
> Date: 2006-12-9 下午7:50
> Subject: Re: [gmx-users] Re: fudgeQQ (again ...) and fudgeLJ
> To: Discussion list for GROMACS users <gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>>
> 
> Hi,
> 
> I have just tested the fudgeQQ and fudgeLJ, and found one problem:
> I use the ffoplsaa force field, and add the atoms I used.(in the 
> ffolpsaanb.itp file, there is no [pairtype] section, and I only add the 
> atom informations:
>               ; name  bond_type    mass    charge   ptype          
> sigma      epsilon
>                opls_966   CT     6     12.01100     0      A    
> 3.40000e-01  4.5770e-01)
>  I write my .itp file by hand, in which in the [ pairs] section, I write 
> the pairs and the function, but don't give the values of C6 and C12, 
> that is,
> [ pairs ]
> ; ai  aj   fu    c6    c12
>    1    5   1
>    1    6   1
> ...........
> 
> In the ffoplsaa.itp, I used
> ; nbfunc     comb-rule    gen-pairs    fudgeLJ   fudgeQQ
>     1              2                yes         0.5      0.8333
> 
> I used different values of fudgeLJ and fudgeQQ in the 4 tests, see the 
> following
>          fudgeLJ        fudgeQQ     result (from .log file):   
> LJ-14            Coulomb-14
> 1.         0.5             0.5                                          
>   1.48e+02        -8.896e+03
> 2          1                1                                           
>      1.96e+02        -1.793e+04
> 3.        0.25            0.25                                          
>    9.58e+01        -4.43e+03                
> 4.          0.5            0.8333                                        
> 1.96e+02       -1.498e+04
> 
> The problem is that the LJ-14 doesn't change with the scaling factor of 
> fudgeLJ. Why?
> 
> Does it mean that I must give the C6 and C12 in the .itp file? If yes, 
> should the C6 and C12 scaled by the scaling factor (0.5) and "gen-pairs 
> = no; fudgeLJ=1" ?
> 
> Another question is that in the .log file, what is the  "Disper. corr."? 
> What is the difference between it and the 1-4 interacion?
> 
> 
> -- 
> Sincerely yours,
> **********************************************
> Baofu Qiao, PhD
> Frankfurt Institute for Advanced Studies
> Max-von-Laue-Str. 1
> 60438 Frankfurt am Main, Germany
> TEL:+49-69-7984-7529
> **********************************************
> 
> 
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read manual about dispersion correction.

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.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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