[gmx-users] Gromacs 4 cannot reach Fmax in energy minimisation when version 3 did
Mark Abraham
Mark.Abraham at anu.edu.au
Wed Jan 19 05:27:30 CET 2011
On 19/01/2011 2:48 PM, Cara Kreck wrote:
> Hi everyone,
>
> I have been trying to reproduce a simulation that I previously ran
> successfully with gromacs 3.3.3 in gromacs 4.0.7 and 4.5.1. It is of a
> tip4p water box generated with Packmol (and no I can't use the already
> provided tip4p water box). However I can't even make it past the
> energy minimisation step. I have noticed that all simulations run into
> trouble at step 12 and 3.3.3 manages to recover, whereas 4.0.7 and
> 4.5.1 get stuck. The results of 4.0.7 and 4.5.1 are identical.
>
> Here's an extract from the 4.0.7/4.5.1 log file:
>
> Step Time Lambda
> 11 11.00000 0.00000
>
> Energies (kJ/mol)
> LJ (SR) Coulomb (SR) Coul. recip. Potential
> Pressure (bar)
> 8.12398e+03 -4.64002e+03 -8.80558e+02 2.60340e+03
> -4.27109e+03
>
> Step Time Lambda
> 12 12.00000 0.00000
>
> Energies (kJ/mol)
> LJ (SR) Coulomb (SR) Coul. recip. Potential
> Pressure (bar)
> 5.67868e+03 -7.67528e+03 -1.19351e+03 -3.19011e+03
> -5.97596e+04
>
> Step Time Lambda
> 13 13.00000 0.00000
>
> Step Time Lambda
> 14 14.00000 0.00000
>
> Step Time Lambda
> 15 15.00000 0.00000
>
> Step Time Lambda
> 16 16.00000 0.00000
>
> Step Time Lambda
> 17 17.00000 0.00000
>
> Step Time Lambda
> 18 18.00000 0.00000
>
> Step Time Lambda
> 19 19.00000 0.00000
>
> Step Time Lambda
> 20 20.00000 0.00000
>
> Step Time Lambda
> 21 21.00000 0.00000
>
> Step Time Lambda
> 22 22.00000 0.00000
>
> Step Time Lambda
> 23 23.00000 0.00000
>
> Step Time Lambda
> 24 24.00000 0.00000
>
> Step Time Lambda
> 25 25.00000 0.00000
>
> Step Time Lambda
> 26 26.00000 0.00000
>
> Step Time Lambda
> 27 27.00000 0.00000
>
> Step Time Lambda
> 28 28.00000 0.00000
>
> Step Time Lambda
> 29 29.00000 0.00000
>
>
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 100
>
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
>
> Steepest Descents converged to machine precision in 30 steps,
> but did not reach the requested Fmax < 100.
> Potential Energy = -3.1901118e+03
> Maximum force = 6.9292950e+05 on atom 97
> Norm of force = 2.1575133e+04
>
>
>
> And from the 3.3.3 log file:
>
> Step Time Lambda
> 11 11.00000 0.00000
>
> Energies (kJ/mol)
> LJ (SR) Coulomb (SR) Coul. recip. Potential
> Kinetic En.
> 8.28949e+03 -4.56483e+03 -8.69953e+02 2.85470e+03
> 0.00000e+00
> Total Energy Temperature Pressure (bar)
> 2.85470e+03 0.00000e+00 0.00000e+00
>
>
> t = 0.012 ps: Water molecule starting at atom 97 can not be settled.
> Check for bad contacts and/or reduce the timestep.Wrote pdb files
> with previous and current coordinates
> Step Time Lambda
> 12 12.00000 0.00000
>
> Step Time Lambda
> 13 13.00000 0.00000
>
> Energies (kJ/mol)
> LJ (SR) Coulomb (SR) Coul. recip. Potential
> Kinetic En.
> 6.60039e+03 -6.11407e+03 -1.08723e+03 -6.00910e+02
> 0.00000e+00
> Total Energy Temperature Pressure (bar)
> -6.00910e+02 0.00000e+00 0.00000e+00
>
> ...
>
> (continued on with a few more similar warnings but eventually settled)
>
> ...
>
> Steepest Descents converged to Fmax < 100 in 233 steps
> Potential Energy = -2.3777645e+04
> Maximum force = 9.8486107e+01 on atom 1393
> Norm of force = 5.2092145e+02
>
>
>
> And here's the input parameters:
>
> cpp = /usr/bin/cpp
> define =
> constraints = all-angles
> unconstrained_start = no
> constraint_algorithm = shake
> shake_tol = 0.0001
> morse = no
> integrator = steep
> nsteps = 1000
> ; Energy minimizing
> emtol = 100
> emstep = 0.01
> nstcomm = 1
> nstlist = 10
> ns_type = grid
> pbc = xyz
> rlist = 0.9
> coulombtype = pme
> rcoulomb = 0.9
> vdw-type = cut-off
> rvdw = 0.9
> nstenergy = 10
> Tcoupl = no
> Pcoupl = no
> gen_vel = no
>
>
>
> I then tried running the same parameters using the spc water box in
> the tutorial and got these results:
>
> 4.0.5/4.7.1
>
> Steepest Descents converged to Fmax < 100 in 63 steps
> Potential Energy = -1.0896633e+04
> Maximum force = 9.1075676e+01 on atom 202
> Norm of force = 1.3547868e+01
>
>
> 3.3.3
>
> Steepest Descents converged to Fmax < 100 in 32 steps
> Potential Energy = -1.0760295e+04
> Maximum force = 8.2715759e+01 on atom 425
> Norm of force = 5.6500586e+02
>
>
> It also gave the same result for version 4 if I ran 4 with the .tpr
> file I had prepared using 3.
>
> I am running these remotely and I didn't know whether single or double
> precision versions were installed. The .trr file from 3.3.3 was twice
> the size of the others (even with half the steps), but gmxdump told me
> that all versions were single precision.
>
> Are the differences simply due changes between the versions? Looking
> at the release notes, most changes (particularly between 3.3.3 and
> 4.0.7) were related to parallelisation and I've run everything on a
> single cpu. Or is there something else I'm missing?
Of itself, I don't think this is a problem. The same software with a
different compiler can change its numerical stability, in extreme cases.
It would be surprising for 4.0 to have introduced an algorithmic change
that breaks EM, and for it to be first noticed now. It is normal not to
run EM with constraints, and I suspect some change in the constraint
implementation may be the origin of your observations. Try without
constraints.
Mark
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