<br><font size=2 face="sans-serif">Hi,</font>
<br>
<br><font size=2 face="sans-serif">while tuning the force kernels for BlueGene
I stumbled across the following.</font>
<br>
<br><font size=2 face="sans-serif">The C (also Fortran) code generated
by mknb for calculating the Buckingham potential is the following:</font>
<br>
<br><font size=2 face="sans-serif"> rinvsq = rinv * rinv</font>
<br><font size=2 face="sans-serif"> br = cexp2 * rsq * rinv</font>
<br><font size=2 face="sans-serif"> Vvdwexp = cexp1 * exp (-br) </font>
<br><font size=2 face="sans-serif"> Vvdw6 = C6 / (rinvsq*rinvsq*rinvsq)</font>
<br><font size=2 face="sans-serif"> fscal = (br * Vvdwexp - 6.0 *
Vvdw6) * rinvsq;</font>
<br>
<br><font size=2 face="sans-serif"> fx = dx * fscal</font>
<br><font size=2 face="sans-serif"> fy = dy * fscal</font>
<br><font size=2 face="sans-serif"> fz = dz * fscal</font>
<br>
<br><font size=2 face="sans-serif">This does not look right to me, because
the br * Vvdwexp part in the calculation of</font>
<br><font size=2 face="sans-serif">fscal should only be scaled by rinv
and not rinvsq as deduced by following calculation:</font>
<br>
<br><font size=2 face="sans-serif">The Buckingham potential is defined
by the following form:</font>
<br>
<br><font size=2 face="sans-serif"> V(r) = C1 * exp ( - C2
* r) - C6 / r**6</font>
<br>
<br><font size=2 face="sans-serif">The force on particle 1 is calculated
by the formula:</font>
<br>
<br><font size=2 face="sans-serif"> Fx = - dx / r * d/dr
V(r)</font>
<br><font size=2 face="sans-serif"> = -dx
/ r * { - C1*C2*r * exp( -C2 * r) + 6.0 * C6 / r**7 }</font>
<br><font size=2 face="sans-serif"> = -dx * {
1/r**2 * 6.0 * C6 / r**6 + 1/r * br * C1 * exp (-C2 * r) }</font>
<br><font size=2 face="sans-serif"> = -dx * {
rinvsq * 6.0 * Vvdw6 + rinv * br * Vvdwexp }</font>
<br>
<br><font size=2 face="sans-serif"> != -dx * rinvsq
* { 6.0 * Vvdw6 + br * Vvdwexp }</font>
<br>
<br><font size=2 face="sans-serif">Am I making a mistake here or is the
GROMACS code wrong ?</font>
<br><font size=2 face="sans-serif"><br>
Viele Grüsse / Best regards,<br>
Dr. Mathias Pütz<br>
<br>
IT Specialist for Application Perfomance<br>
<br>
Deep Computing - Strategic Growth Business<br>
IBM Systems & Technology Group<br>
<br>
e-mail: mpuetz@de.ibm.com<br>
mobile: + 49-(0)160-7120602<br>
fax: + 49-(0)6131-84-6660<br>
<br>
snailmail:<br>
IBM Deutschland GmbH<br>
Department B458<br>
Hechtsheimer Str. 2 / Building 12<br>
55131 Mainz<br>
Germany<br>
</font>