[gmx-developers] Reaction Filed crash!

[Chris Neale]

You might be experiencing the same thing that was discussed on the users 
list in September:

http://lists.gromacs.org/pipermail/gmx-users/2011-September/064236.html
http://lists.gromacs.org/pipermail/gmx-users/2011-September/064237.html

The conclusion there was to use a small nstpcouple (perhaps =1) during 
equilibration.

Chris.

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 
> (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 
> (http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation 
> <http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation?highlight=constant+pH>).
>
> 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.
>
> Regards,
> Miguel
>
> -- 
> ============================================
> 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
> ______________________________________________
>

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