[gmx-users] Tabscale

[David]

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
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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