[gmx-users] Energy Minimisation and Equilibration Problems

Bruce D. Ray brucedray at yahoo.com
Fri Aug 7 14:06:02 CEST 2009

On Thursday, August 6, 2009 at 7:59:43 PM Nancy <nancy5villa at 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.


Bruce D. Ray, Ph.D.
Associate Scientist
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273

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