[gmx-users] Energy minimisation with different water models
spoel at xray.bmc.uu.se
Fri Apr 22 22:03:01 CEST 2005
On Fri, 2005-04-22 at 19:51 +0000, Tomek R wrote:
> This topic was already touched on the list, but I have not found any
> solution to it. I am running a simple steepest descent energy minimisation
> (em.mdp input file like in speptide tutorial) on a AAA tripeptide /OPLSAA
> forcefield, GROMACS 3.2.1 and I am getting the following results on
> different water models:
> It converges well with SPC / TIP5P, but something goes very wrong with
> TIP4P. What's the problem?
probably a Hydrogen was fatally attracted to a negative charge (or
oxygen). If the H is close enough to an O there is a singularity in the
potential... Try slightly different starting coordinates for the atom
involved and/or check your coords.
> Step= 42, Dmax= 1.6e-02 nm, Epot= -3.86495e+04 Fmax= 1.11394e+04, atom= 5
> Step= 44, Dmax= 9.6e-03 nm, Epot= -3.88441e+04 Fmax= 1.82268e+03, atom= 5
> Steepest Descents converged to Fmax < 2000 in 45 steps
> Potential Energy = -3.8844137e+04
> Maximum force = 1.8226837e+03 on atom 5
> Norm of force = 7.5002910e+03
> Step= 28, Dmax= 2.7e-06 nm, Epot= -1.39090e+08 Fmax= 2.16801e+14, atom=
> Step= 30, Dmax= 1.6e-06 nm, Epot= -3.75909e+07 Fmax= 2.45911e+13, atom=
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 2000
> Double precision normally gives you higher accuracy.
> Steepest Descents converged to machine precision in 31 steps,
> but did not reach the requested Fmax < 2000.
> Potential Energy = -1.3909030e+08
> Maximum force = 2.1680114e+14 on atom 1656
> Norm of force = 2.8675946e+14
> Step= 33, Dmax= 7.5e-03 nm, Epot= -9.64603e+03 Fmax= 4.13647e+03, atom= 35
> Step= 35, Dmax= 4.5e-03 nm, Epot= -9.67248e+03 Fmax= 1.89664e+03, atom= 35
> Steepest Descents converged to Fmax < 2000 in 36 steps
> Potential Energy = -9.6724756e+03
> Maximum force = 1.8966361e+03 on atom 35
> Norm of force = 2.5414328e+04
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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://xray.bmc.uu.se/~spoel
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