[gmx-users] neighborsearching in semiisotropic systems
Berk Hess
gmx3 at hotmail.com
Wed Jun 4 12:37:43 CEST 2008
Hi,
I have not heard of any code problems with pressure coupling.
But in general things can get unstable when you couple to quickly.
0.5 ps is quite short, but should be ok for isotropic coupling in water.
For semiistropic coupling it might actually be too fast, I have never
tried this. Semiisotropic coupling will lead to larger and faster
fluctuations.
For the large system I would set tau_p to somewhere between 1 and 5 fs.
I don't know if you compressibility value is reasonable when you have
a membrane in it, but I guess it would not be to far off.
One last thing, don't you want to use surface tension coupling?
Berk.
> Date: Wed, 4 Jun 2008 11:54:53 +0200
> From: till at bph.rub.de
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] neighborsearching in semiisotropic systems
>
> Hi Berk,
> the whole system I want to simulate contents a membrane (that's why I
> use semiisotropic pressure coupling) and this system crashed with the
> same error message.
> In the membrane system and in the small test system no distortion of the
> box can be observed during the simulation. The cubic form of the box is
> stable.
>
>
> Step Time Lambda
> 1555000 3110.00000 0.00000
>
> Rel. Constraint Deviation: Max between atoms RMS
> Before LINCS 0.016766 46 47 0.003642
> After LINCS 0.000042 23 25 0.000013
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 1.61040e+02 6.05084e+01 3.35858e+01 1.03030e+01 1.32855e+03
> LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. Potential
> 2.25304e+04 -6.11549e+02 -1.40294e+05 -1.72589e+04 -1.34040e+05
> Kinetic En. Total Energy Temperature Pressure (bar)
> 2.39730e+04 -1.10067e+05 2.97751e+02 -1.18958e+02
>
> Grid: 6 x 6 x 8 cells
> Grid: 5 x 5 x 8 cells
> Grid: 6 x 6 x 8 cells
> Grid: 5 x 5 x 8 cells
> Grid: 6 x 6 x 8 cells
> Grid: 5 x 5 x 8 cells
> Grid: 6 x 6 x 8 cells
> Grid: 5 x 5 x 8 cells
> -------------------------------------------------------
> Program mdrun_d.mpi, VERSION 3.3.1
> Source code file: nsgrid.c, line: 226
>
> Range checking error:
> Explanation: During neighborsearching, we assign each particle to a grid
> based on its coordinates. If your system contains collisions or parameter
> errors that give particles very high velocities you might end up with some
> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
> put these on a grid, so this is usually where we detect those errors.
> Make sure your system is properly energy-minimized and that the potential
> energy seems reasonable before trying again.
>
> Variable ci has value 284. It should have been within [ 0 .. 200 ]
> Please report this to the mailing list (gmx-users at gromacs.org)
> -------------------------------------------------------
>
>
> I have no explanation why the system with semiisotropic pressure
> coupling crashes within the 10ns simulation with tau_p=0.5 and does not
> crash with tau_p=5.0. The other problem is starting two identical
> simulations the systems crashed at different timesteps.
>
> Till
>
> Berk Hess schrieb:
> > Hi,
> >
> > Did you check how your box dimensions evolve?
> >
> > For a homogeneous system (as your small test system)
> > one should not use semi or anisotropic pressure coupling,
> > since the box shape can distort unlimitedly causing
> > the system to crash.
> >
> > Berk.
> >
> >
> > ------------------------------------------------------------------------
> > > Date: Tue, 3 Jun 2008 17:00:14 +0200
> > > From: till at bph.rub.de
> > > To: gmx-users at gromacs.org
> > > Subject: [gmx-users] neighborsearching in semiisotropic systems
> > >
> > > Dear users,
> > >
> > > During protein simulations occurred the range checking error of the
> > > neighborsearching. I checked the comments on this mistake in the user
> > > list and then checked my system on any hints of an exploding system but
> > > it seems to be stable. In order to be sure I cut down the system to a
> > > small peptide consisting of only ten aminoacids and used the ffG43a1
> > > forcefield.
> > >
> > >
> > > I performed 10ns simulations of this small system in a cubic
> > > spc-waterbox with different pressure parameters and tried single and
> > > double precision. I got the following results:
> > >
> > >
> > > For
> > >
> > > pcoupltype = semiisotropic
> > >
> > > tau_p = 0.5 0.5
> > >
> > > compressibility = 4.5E-5 4.5E-5
> > >
> > > ref_p = 1 1
> > >
> > >
> > > with double precision occurred the mistake:
> > >
> > >
> > > -------------------------------------------------------
> > >
> > > Program mdrun_d.mpi, VERSION 3.3.1
> > >
> > > Source code file: nsgrid.c, line: 226
> > >
> > >
> > > Range checking error:
> > >
> > > Explanation: During neighborsearching, we assign each particle to a grid
> > >
> > > based on its coordinates. If your system contains collisions or parameter
> > >
> > > errors that give particles very high velocities you might end up with
> > some
> > >
> > > coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
> > >
> > > put these on a grid, so this is usually where we detect those errors.
> > >
> > > Make sure your system is properly energy-minimized and that the potential
> > >
> > > energy seems reasonable before trying again.
> > >
> > >
> > > Variable ci has value 284. It should have been within [ 0 .. 200 ]
> > >
> > > Please report this to the mailing list (gmx-users at gromacs.org
> > > <mailto:gmx-users at gromacs.org>)
> > >
> > >
> > > Then, I changed tau_p to 5.0 and the mistake did not occurce anymore
> > > during the 10 ns. With single precision the mistake never occurres. I
> > > also tested double precision with pcoupltype = isotropic and this also
> > > works.
> > >
> > > Next, I wanted to reproduce the mistake so I took the same tpr file of
> > > the crashed simulation with tau_p = 0.5 and started the simulation
> > > again. The mistake occurred again but not at the same timestep. The
> > > first run crashed after step 1558630 and the second run after step
> > > 2597500 and also the ci variable is not exactly the same (Variable ci
> > > has value 283. It should have been within [ 0 .. 200 ]).
> > >
> > >
> > > I think there might be a problem between the neighborsearching and the
> > > semiisotropic pressurcoupling together with double precision. I am quite
> > > sure that the peptide is not the problem. Maybe there is a problem with
> > > a water molecule. I would be glad if someone can give me an explanation
> > > why this mistake is not reproducable at the same timestep and why it
> > > occures with tau_p=0.5 and not with tau_p=5.0.
> > >
> > >
> > > Thanks
> > >
> > >
> > > Till
> > >
> > > _______________________________________________
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