[gmx-developers] Reaction Filed crash!
machuque at fc.ul.pt
Mon Oct 3 18:53:59 CEST 2011
Hi to all developers,
We have been using GMX here in the group for almost a decade and we are
familiar with almost all versions of the package.
Recently, when testing the newer versions (4.5.x) using Reaction Field
in a simple lysozyme system (4LZT), my system crashed constantly.
System: 4LZT (129 a.a.) directly from PDB databank.
Water: ~6250 molecules
GMX: 4.5.x (all versions tested)
ForceField: Gromos 53A6
Long range elect.: RF, RF-nec, GRF or simply "Cutoff" (all with same
Ensemble: NPT or NVT
So, what do we already know about the problem:
- The crash always starts in the NH bond present in the amides (main
chain or side chains of GLN and ASN). In the stepxxxx.pdb, we observe
the hydrogen jumping out of place.
- The stability of the simulation is dependent on the quality of the
minimization/initialization procedure. Simple/regular procedures leads
to crashs within 10 ns of simulation. More elaborate protocols of
minimization/initialization can delay the crashs a little longer.
- The system crashes independently of the number of "threads" used (1-12).
- The instability only leads to crashs when dealing with proteins >100
a.a.. Simulating a 15 a.a. peptide for over 1 microsecond does not lead
to a crash.
- No problem/crash is observed when using PME.
- No problem/crash is observed when using GMX versions prior to 4.0.7.
My question is this, what might have happen with the RF code between
versions 4.0.x and 4.5.x that leads to this problem? Or is there any
specific parameter to be used with RF/Cutoff to avoid these problems?
Even though RF is not very popular with GMX developers, it has been
essential for the development of our in house Constant-pH MD method
On a typical MD run we use the following MDP file, or a similar one.
integrator = md
tinit = 0
dt = 0.002
nsteps = 5000000
comm-mode = Linear
nstcomm = 1
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 5000
nstenergy = 5000
nstxtcout = 5000
xtc-precision = 1000
energygrps = Protein SOL
nstlist = 5
ns_type = grid
pbc = xyz
periodic_molecules = no
rlist = 0.9
coulombtype = Reaction-Field
rcoulomb-switch = 0
rcoulomb = 1.4
epsilon_r = 1
epsilon_rf = 54
vdwtype = Cut-off
rvdw-switch = 0
rvdw = 1.4
DispCorr = No
tcoupl = berendsen
tc-grps = Protein SOL
tau-t = 0.1 0.1
ref-t = 298.15 298.15
Pcoupl = berendsen
Pcoupltype = Isotropic
tau-p = 0.5
compressibility = 4.5e-5
ref-p = 1
refcoord_scaling = No
gen_vel = no
constraints = all-bonds
constraint_algorithm = lincs
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 90
Thank you for any help you can assist us.
Department of Chemistry and Biochemistry
Faculty of Sciences, University of Lisbon
Campo Grande, Edifício C8 (sala 8.5.47)
1749-016 Lisboa, Portugal
Tel. : +351 217500112 (int.ext.28547)
Mobile: +351 967562285
E-mail: machuque at fc.ul.pt
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