[gmx-users] Buckingham potential

[David]

On Tue, 2004-01-27 at 08:45, Stefano Piana wrote:
> Hallo,
> I am trying to perform a calculation with a Buckingham potential,
> however I always get Nan in the energy of my system.
> I also tried to put all the parameters of the Buck pot to 0. I still get
> Nan. On the other hand if I set my nbfunct to 1 (that is LJ) with all
> the parameters set to 0 (which should be the same as Buck pot with all
> parameters to 0) I get "reasonable" numbers out of the calculation.
check your tpr file. the parameters may be nonsensical. if you specifiy
reasonable values under
[ nonbond_params ]

it should work. please note the units should be nm and kJ/mol
> 
> these are the input and outputs:
> --------------- Input Buckingham ------------------------
> #define _FF_GROMOS
> #define _FF_GROMOS96
> 
> 
> 
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
>        2       1        yes      0.0     0.0
> 
> 
> 
> [ atomtypes ]
> C         1.00000       0.000       A 0.00000E+00 0.00000E+00 0.00000E+00
> O         1.00000       0.000       A 0.00000E+00 0.00000E+00 0.00000E+00
> Mg        1.00000       0.000       A 0.00000E+00 0.00000E+00 0.00000E+00
> Ox        1.00000       0.000       A 0.00000E+00 0.00000E+00 0.00000E+00
> 
> 
> 
> [ nonbond_params ]
> C    C         2   0.000000E+00   0.000000E+00   0.000000E+00
> C    O         2   0.000000E+00   0.000000E+00   0.000000E+00
> C    Mg        2   0.000000E+00   0.000000E+00   0.000000E+00
> C    Ox        2   0.000000E+00   0.000000E+00   0.000000E+00
> O    O         2   0.000000E+00   0.000000E+00   0.000000E+00
> O    Mg        2   0.000000E+00   0.000000E+00   0.000000E+00
> O    Ox        2   0.000000E+00   0.000000E+00   0.000000E+00
> Mg   Mg        2   0.000000E+00   0.000000E+00   0.000000E+00
> Mg   Ox        2   0.000000E+00   0.000000E+00   0.000000E+00
> Ox   Ox        2   0.000000E+00   0.000000E+00   0.000000E-00
> 
> --------------------- Output Buckingham ----------------------------
> 
> Steepest Descents did not converge in 2 steps
>     Potential Energy  =          nan
> Maximum force:  1.38452e+04
> 
> ---------------------Input LJ --------------------------------------
> #define _FF_GROMOS
> #define _FF_GROMOS96
> 
> 
> 
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
>        1       1        yes      0.0     0.0
> 
> 
> 
> [ atomtypes ]
> C         1.00000       0.000       A 0.00000E+00 0.00000E+00
> O         1.00000       0.000       A 0.00000E+00 0.00000E+00
> Mg        1.00000       0.000       A 0.00000E+00 0.00000E+00
> Ox        1.00000       0.000       A 0.00000E+00 0.00000E+00
> 
> ------------------- Output LJ ---------------------------------------
> 
> Steepest Descents did not converge in 2 steps
> Potential Energy  = -1.26825e+06
> Maximum force:  1.97743e+04
> 
> ---------------------------------------------------------------------
> 
> I have tried all the possible combination of Coulomb interactions and
> also NS search and periodic-nonperiodic system.
> It really looks like the problem is switching on the Buckingham
> potential. I noticed that in the logfile these lines appear:
> 
> Determining largest Buckingham b parameter for table
> Buckingham b parameters, min: 0, max: 83.3333
> Generated table with 500 data points for COUL.
> Tabscale = 500 points/nm
> Generated table with 500 data points for LJ6.
> Tabscale = 500 points/nm
> Generated table with 500 data points for EXPMIN.
> Tabscale = 0 points/nm
> 
> It looks like the table for the Buck potential is not generated at all!
> This might be related to a change in the code that has been done time
> ago to save some memory and that was reported on the mailing list. I
> don't know if this is the reason for the weird behaviour...
> I would like to know if anybody in the list that has been successful in
> running calculations with a Buckingham potential with Gromacs 3.1.4
> could send me some input files with coordinates in such a way that I can
> test it on my Linux box.
> Any kind of suggestion is warmly welcome!
> 
> Stefano
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel
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