[gmx-developers] Reaction Filed crash!
machuque at fc.ul.pt
Mon Oct 3 20:38:19 CEST 2011
Thank you Justin and Chris for your comments.
We did follow that thread and we did prepare very complex initialization
procedures using "nstpcouple=1" which increased the stability of our
simulation. Nevertheless, in all my production runs the simulations
crashed. We have a few tests running at the moment (already 20 ns) that
are surviving for now. But you have to agree that something must be
wrong when, using such a long/smooth initialization (and with
nstpcouple=1), some systems are surviving and others are already dead.
I don't know if Itamar Kass managed to solve all his problems just by
"doing a better initialization", but I can assure you that we can't.
I am really curious that noone else has bumped into this one. Is there
noone else using Reaction Field this days in the GMX community?
I would appreciate any examples from people that have successfully
simulate MD of a protein with RF.
On 03-10-2011 18:33, Chris Neale wrote:
> 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 03-10-2011 18:34, Justin A. Lemkul wrote:
> 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 (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.
> Sporadic crashes have been reported for systems that are stable under 4.0.x and
> not 4.5.x. The solution that seems to have worked is to adjust the nsttcouple
> and nstpcouple values. See the discussion here (and subsequent posts in the
>> 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
>> www1: http://webpages.fc.ul.pt/~mamachuqueiro
>> www2: http://intheochem.fc.ul.pt
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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