[gmx-users] Energy Minimisation and Equilibration Problems

[Bruce D. Ray]

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.


Sincerely,


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



      
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