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?
Any help would be greatly appreciated.
Thanks,
Cara
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