[gmx-users] Re: stepsize too small ... but potential energy negative!
Justin A. Lemkul
jalemkul at vt.edu
Mon May 24 16:08:27 CEST 2010
Anna Marabotti wrote:
> Dear Justin, dear Luca,
> here's the answer to your questions:
> - I'm currently using the "classical" forcefield gromos96 43a1 (choice "0"
> in pdb2gmx). After producing the topology, the only warning I see from
> pdb2gmx is this one: WARNING: there were 0 atoms with zero occupancy and 63
> atoms with occupancy unequal to one (out of 1583 atoms). Check your pdb
> However, atoms with occupancy <1 are present also in "regular" PDB files (if
> I remember well, also in PDB files I used previously). Is this a problem?
> - Box: I'm currently using a cubic box and I'm setting 1 nm of distance
> between solute and box with option -d (and also center the box). Looking at
> the system I can't see any contact between the protein and the box walls. I
> started by setting 0.8 nm and the problem was the same.
> - .mdp file: here it is:
> cpp =
> define = -DFLEXIBLE
> constraints = none
> integrator = steep
> nsteps = 50000
> emtol = 1000
> emstep = 0.1
This step size is far too large! Try something more like 0.01.
> nstlist = 5
> ns_type = grid
> rlist = 1.0
> coulombtype = PME
> rcoulomb = 1.0
> rvdw = 1.2
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> Tcoupl = no
> Pcoupl = no
> gen_vel = no
> It's very similar to the one Justin suggested in its tutorial.
...except for numerous changes.
> - PR-MD: I'not interested in skipping the minimization and continue with MD.
> I tried to launch a PR-MD step to see if the error produced in this step was
> more informative, and try to understand what was the problem on my
> structure. I failed, however...
> I would also add that this is not the first time that I'm using an homology
> model produced by MODELLER to perform MD. All the checks I made on my model
> tell me that it is a good model, so I really don't understand what's wrong
> with it.
> Finally, I started from the structure deprived of the first residue in order
> to see if that residue was the "bad" one, but the problem still persists and
> the potential energy has the same negative value with the same order of
Likely due to a flawed .mdp file. The algorithm is trying to take too large of
a step along the potential energy surface, causing bad geometry and infinite
forces. A bit more finesse should solve this problem.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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