[gmx-users] Tabscale again

[Yuguang Mu]

Dear Eric, David,

Due to the systematic difference of PME long range Coulomb energy
between single and double precision, which is 1000 times larger than other
terms.

What could be the reason ?

Could be the Table routines are used for coulomb: TRUE ?
That in single  500 points/nm
     in double 2000 points/nm ?


or something else in the FFTW routine ?

Dr. Yuguang Mu
Institute for Physical and Theoretical Chemistry
J.W. Goethe University Frankfurt am Main
Marie Curie Str. 11
60439 Frankfurt/Main, Germany
Tel: +49-(0)69-798-29711

On 17 Sep 2003, David wrote:

> On Wed, 2003-09-17 at 12:37, Yuguang Mu wrote:
> > Dear Erik,
> > The question I really want to ask is that why the virial calculated from
> > the same trajectory but using different precisions are quite different.
> >
> > I have a trajectory simulated in single precision, then I use -rerun
> > switch to recalculate energies in double precision.
> >
> > The potentials, kinetics, terms turn out nearly exactly same, but I found
> > the virial, also, the pressure, specially the off-diagonal terms, deviate
> > greatly.
> >
> > In other words, if we eqilibrate the system in single precision with
> > pressure coupling (orthogonal box but with anisotropy coupling), the
> > final shape of the box will be greatly different from that simulated with
> > double precision using the same protocol.
> >
> > I donot think it tolerant.
> >
> > Is it possible that in the formula of virial calculations there happens
> > somehow overflow inthe case of single precision ?
>
> I don't think so. It is just lack of precision which leads to another
> trajectory. If you have anisotropic scaling you must increase tau_p to
> at least 5 ps. Even then two different trajectories may give you
> different final box size. Try e.g. to run two double precision runs with
> different starting velocities and see how the box evolves.
>
> >
> > Dr. Yuguang Mu
> > Institute for Physical and Theoretical Chemistry
> > J.W. Goethe University Frankfurt am Main
> > Marie Curie Str. 11
> > 60439 Frankfurt/Main, Germany
> > Tel: +49-(0)69-798-29711
> >
> > On Tue, 16 Sep 2003, Erik Lindahl wrote:
> >
> > > Hi,
> > >
> > > Not without hacking the code. The tabscale is selected as 500 points/nm
> > > in single and 2000 points/nm in double. With the cubic spline
> > > interpolation, this essentially gives you full single precision
> > > accuracy, and almost full double precision accuracy for all common
> > > potential forms, respectively.
> > >
> > > Cheers,
> > >
> > > Erik
> > >
> > >
> > > On Tuesday, September 16, 2003, at 09:26 AM, Yuguang Mu wrote:
> > >
> > > > Hi All,
> > > > Inthe log file always printed out the following lines:
> > > >
> > > > Table routines are used for coulomb: TRUE
> > > > Table routines are used for vdw:     FALSE
> > > > Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
> > > > Cut-off's:   NS: 1   Coulomb: 1   LJ: 1
> > > > Generated table with 2000 data points for COUL.
> > > > Tabscale = 2000 points/nm
> > > > Generated table with 2000 data points for LJ6.
> > > > Tabscale = 2000 points/nm
> > > > Generated table with 2000 data points for LJ12.
> > > > Tabscale = 2000 points/nm
> > > > Generated table with 3200 data points for Ewald.
> > > > Tabscale = 2000 points/nm
> > > > Generated table with 3200 data points for LJ6.
> > > > Tabscale = 2000 points/nm
> > > > Generated table with 3200 data points for LJ12.
> > > > Tabscale = 2000 points/nm
> > > >
> > > > here i sthe question, could I change the Tabscale manually ?
> > > >
> > > >
> > > > Dr. Yuguang Mu
> > > > Institute for Physical and Theoretical Chemistry
> > > > J.W. Goethe University Frankfurt am Main
> > > > Marie Curie Str. 11
> > > > 60439 Frankfurt/Main, Germany
> > > > Tel: +49-(0)69-798-29711
> > > >
> > > >
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> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
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