On Thursday, August 6, 2009 at 7:59:43 PM Nancy <nancy5vi...@gmail.com> wrote:
> I ran the minimisation, and mdrun gave the following last few lines of output:
>
> ==================================
> Step=19990, Dmax= 7.8e-06 nm, Epot= -7.14922e+04 Fmax= 3.19585e+04, atom= 2395
> Step=19992, Dmax= 4.7e-06 nm, Epot= -7.14924e+04 Fmax= 8.72456e+03, atom= 2395
>
Step=19993, Dmax= 5.6e-06 nm, Epot= -7.14927e+04 Fmax= 3.70693e+04, atom= 2395
> Step=19994, Dmax= 6.8e-06 nm, Epot= -7.14929e+04 Fmax= 2.10513e+04, atom= 2395
> Step=19995, Dmax= 8.1e-06 nm, Epot= -7.14929e+04 Fmax= 4.71234e+04, atom= 2395
>
Step=19996, Dmax= 9.7e-06 nm, Epot= -7.14931e+04 Fmax= 3.68827e+04, atom= 2395
> Step=19998, Dmax= 5.8e-06 nm, Epot= -7.14933e+04 Fmax= 1.35461e+04, atom= 2395
> Step=19999, Dmax= 7.0e-06 nm, Epot= -7.14933e+04 Fmax= 4.77130e+04, atom= 2395
>
Step=20000, Dmax= 8.4e-06 nm, Epot= -7.14936e+04 Fmax= 2.41860e+04, atom= 2395
>
> writing lowest energy coordinates.
>
> Steepest Descents did not converge to Fmax < 10 in 20001 steps.
> Potential Energy = -7.1493609e+04
>
Maximum force = 2.4185994e+04 on atom 2395
> Norm of force = 8.1511212e+02
> ==================================
>
> As you can be seen, the forces still do not converge to Fmax < 10, even after
> 20,000 steps.
>
> Does anyone know what the problem might be?
The problem is my error in the specification of non-bonded interaction
combination rules,
FudgeLJ, and FudgeQQ for gromacs force fields.
Line 7 of your file ffethanediol.itp currently reads:
1 2 yes 0.5 0.833333
This was taken from ambconv and is correct for amber and gaff force fields, but
not
for gromacs force fields, nor for OPLS-AA.
Change line 7 of the file ffethanediol.itp to read:
1 1 no 1.0 1.0
The correction is in topolbuild 1.3 which is not yet released, but this error
was not caught
for the topolbuild 1.2 series. Quite frankly, I had forgotten that
modification was made as
I've been editing the set of tables needed to add OPLS-AA to the mix of force
fields available.
As a general note. For gromacs force field topologies generated with anything
in the
topolbuild 1.2 series, this edit to the itp file that specifies the defaults is
required.
Sincerely,
--
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN 46202-3273
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