[gmx-users] Re: stepsize too small ... but potential energy negative!

Anna Marabotti anna.marabotti at isa.cnr.it
Mon May 24 15:44:19 CEST 2010

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
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.
- 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


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