[gmx-developers] Reaction Filed crash!
chris.neale at utoronto.ca
Mon Oct 3 19:33:24 CEST 2011
You might be experiencing the same thing that was discussed on the users
list in September:
The conclusion there was to use a small nstpcouple (perhaps =1) during
On 11-10-03 12:53 PM, Miguel Machuqueiro wrote:
> 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
> fate.. crash!)
> 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
> - 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.
> Miguel Machuqueiro
> 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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