Mathias PUETZ wrote:
>
> Hi David,
>
> sorry, I found my mistake: the factor of r in my derivate of the exp()
> is incorrect and then the generated GROMACS code is actually correct.
>
Nevermind, we are very happy to have people look at the code with their
eyes open.
> Mathias PUETZ wrote:
> >/
> />/ Hi,
> />/
> />/ while tuning the force kernels for BlueGene I stumbled across the
> />/ following.
> />/
> />/ The C (also Fortran) code generated by mknb for calculating the
> />/ Buckingham potential is the following:
> />/
> />/ rinvsq = rinv * rinv
> />/ br = cexp2 * rsq * rinv
> />/ Vvdwexp = cexp1 * exp (-br)
> />/ Vvdw6 = C6 / (rinvsq*rinvsq*rinvsq)
> />/ fscal = (br * Vvdwexp - 6.0 * Vvdw6) * rinvsq;
> />/
> />/ fx = dx * fscal
> />/ fy = dy * fscal
> />/ fz = dz * fscal
> />/
> />/ This does not look right to me, because the br * Vvdwexp part in the
> />/ calculation of
> />/ fscal should only be scaled by rinv and not rinvsq as deduced by
> />/ following calculation:
> />/
> />/ The Buckingham potential is defined by the following form:
> />/
> />/ V(r) = C1 * exp ( - C2 * r) - C6 / r**6
> />/
> />/ The force on particle 1 is calculated by the formula:
> />/
> />/ Fx = - dx / r * d/dr V(r)
> />/ = -dx / r * { - C1*C2*r * exp( -C2 * r) + 6.0 * C6 / r**7 }
> />/ = -dx * { 1/r**2 * 6.0 * C6 / r**6 + 1/r * br * C1 * exp (-C2
> />/ * r) }
> />/ = -dx * { rinvsq * 6.0 * Vvdw6 + rinv * br * Vvdwexp }
> />/
> />/ != -dx * rinvsq * { 6.0 * Vvdw6 + br * Vvdwexp }
> />/
> />/ Am I making a mistake here or is the GROMACS code wrong ?
> />/
> />/ Viele Grüsse / Best regards,
> />/ Dr. Mathias Pütz
> />/
> />/ IT Specialist for Application Perfomance
> />/
> />/ Deep Computing - Strategic Growth Business
> />/ IBM Systems & Technology Group
> />/
> />/ e-mail: //_mpuetz at de.ibm.com_/
> <http://www.gromacs.org/mailman/listinfo/gmx-developers>/
> />/ mobile: + 49-(0)160-7120602
> />/ fax: + 49-(0)6131-84-6660
> />/
> />/ snailmail:
> />/ IBM Deutschland GmbH
> />/ Department B458
> />/ Hechtsheimer Str. 2 / Building 12
> />/ 55131 Mainz
> />/ Germany
> />/
> />/
> />/ ------------------------------------------------------------------------
> />/
> />/ _______________________________________________
> />/ gmx-developers mailing list
> />/ //_gmx-developers at gromacs.org_/
> <http://www.gromacs.org/mailman/listinfo/gmx-developers>/
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> gromacs.org._/ <http://www.gromacs.org/mailman/listinfo/gmx-developers>/
> /I think it is correct because there is an extra r in the br term.
>
> --
> 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_
> <http://www.gromacs.org/mailman/listinfo/gmx-developers>
> _spoel at gromacs.org_
> <http://www.gromacs.org/mailman/listinfo/gmx-developers>
> _http://folding.bmc.uu.se_ <http://folding.bmc.uu.se/>
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> Viele Grüsse / Best regards,
> Dr. Mathias Pütz
>
> IT Specialist for Application Perfomance
>
> Deep Computing - Strategic Growth Business
> IBM Systems & Technology Group
>
> e-mail: mpuetz at de.ibm.com
> mobile: + 49-(0)160-7120602
> fax: + 49-(0)6131-84-6660
>
> snailmail:
> IBM Deutschland GmbH
> Department B458
> Hechtsheimer Str. 2 / Building 12
> 55131 Mainz
> Germany
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
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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://folding.bmc.uu.se
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