[gmx-developers] Bug in Ewald Code?

[David van der Spoel]

On Tue, 31 Oct 2006, Dave Rogers wrote:

>Developers,
>
>Problem:
>  The ewald potential of the input configuration changes from
>sr=0.000000   recip=-0.094927 to sr=-460.603673 recip=-330.965952 for
>a single water molecule (all system files included below) when the
>bond type ([bonds] funct) is changed from 1 (default) to 6 (harmonic)
>for both of the bonds in Voth's water model!  For now I am unable to
>reproduce his numbers for that water model as he used a harmonic bond
>potential.
>
>Thanks for looking into this,

please add exclusions manually and see if that resolves it. submit a 
bugzilla anyway,

>~ David Rogers
>
>  Version: gromacs 3.3.1 compiled with options (which uses fftw3 by default):
>./configure --prefix=/usr/local --enable-mpi --disable-float
>--with-external-blas --with-external-lapack --program-suffix=
>## --------- ##
>## Platform. ##
>## --------- ##
>
>hostname = yogen.cros.uc.edu
>uname -m = x86_64
>uname -r = 2.6.17-prepYOGEN
>uname -s = Linux
>uname -v = #2 SMP Wed Aug 23 13:04:18 EDT 2006
>
>Files:
>
><FILE: flex_voth.itp>
>[ moleculetype ]
>; molname       nrexcl
>SOL             2
>
>[ atoms ]
>;   nr   type  resnr residue  atom   cgnr     charge       mass
>     1     OW      1    SOL     OW      1      -0.82
>     2     HW      1    SOL    HW1      1       0.41
>     3     HW      1    SOL    HW2      1       0.41
>
>[ bonds ]
>; i     j       funct   length  force.c.
>1       2       1       0.1012  443153.3808
>1       3       1       0.1012  443153.3808
>
>[ angles ]
>; i     j       k       funct   angle   force.c.
>2       1       3       1       113.24  317.5656
></FILE>
>
><FILE: topol.top>
>#include "ffgmx.itp"
>#include "flex_voth.itp"
>
>[ system ]
>Pure Water
>
>[ molecules ]
>SOL     1
></FILE>
>
><FILE: gro.mdp>
>; MDP for computing Voth's flex-spc model properties with Gromacs.
>
>; VARIOUS PREPROCESSING OPTIONS
>title                    = Yo
>cpp                      = /usr/bin/cpp
>include                  =
>define                   =
>
>; RUN CONTROL PARAMETERS
>integrator               = md
>dt                       = 0.001
>nsteps                   = 1
>tinit                    = 0
>
>comm-mode                = Linear
>nstcomm                  = 1
>
>nstxout                  = 1
>nstvout                  = 1
>nstfout                  = 1
>
>nstlog                   = 1
>nstenergy                = 1
>
>nstlist                  = 1
>ns_type                  = simple
>pbc                      = xyz
>domain-decomposition     = no
>
>coulombtype              = PME
>rcoulomb                 = 0.9
>vdw-type                 = Cut-off
>rvdw                     = 0.9
>rlist                    = 0.9
>
>pme_order                = 6
>ewald_rtol               = 3.95403e-8
>optimize_fft             = no
>; FFT grid size, when a value is 0 fourierspacing will be used
>fourier_nx               = 32
>fourier_ny               = 32
>fourier_nz               = 32
></FILE>
>
><FILE: wat.pdb>
>TITLE     Single, lonely water molecule
>REMARK    THIS IS A SIMULATION BOX
>CRYST1   19.000   19.000   19.000  90.00  90.00  90.00 P 1           1
>MODEL        1
>ATOM      1  OW  SOL     1       2.300   6.280   1.130  1.00  0.00
>ATOM      2  HW1 SOL     1       1.370   6.260   1.500  1.00  0.00
>ATOM      3  HW2 SOL     1       2.310   5.890   0.210  1.00  0.00
>ENDMDL
></FILE>
>
><FILE: run.sh>
>#!/bin/sh
>
>grompp -f gro.mdp -c wat.pdb -o gro.tpr
>mdrun -s gro.tpr -g gro -e gro -o gro -c gro
>cat <<END | g_energy -f gro.edr -o gro.en.xvg
>Bond
>Angle
>LJ-(SR)
>Coulomb-(SR)
>Coul.-recip.
>Potential
>Kinetic-En.
>Pressure-(bar)
>Vir-XX
>Vir-YY
>Vir-ZZ
>
>END
>
>cat gro.en.xvg
></FILE>
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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