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Hi Johannes,<br>
<br>
Thanks for the correction - you're right of course (when deltaX = 1
it's the same).<br>
<br>
To be closer to the gromacs code it's <br>
der = (y[N+1] - y[N-1]) * 0.5 * tabscale<br>
<br>
where <br>
tabscale = number of points per nm (or degree for angles/dihedrals).<br>
<br>
Ran.<br>
<br>
Johannes Kamp wrote:
<blockquote cite="mid4A6871B7.9090404@rwth-aachen.de" type="cite">
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Hi Ran,<br>
<br>
are you sure the derivative is calculated as:<br>
der = (y[N+1] - y[N-1]) * 0.5 * deltaX<br>
<br>
and not as:<br>
der = (y[N+1] - y[N-1]) * 0.5 / deltaX ?<br>
<br>
The last calculation makes a little more sense to me...<br>
<br>
-Johannes<br>
<br>
<br>
<blockquote
cite="mid:20090721140956.3F63F246CA@struktbio205.bmc.uu.se" type="cite">
<blockquote cite="mid280792.44938.qm@web15302.mail.cnb.yahoo.com"
type="cite">
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<div
style="font-family: times new roman,new york,times,serif; font-size: 12pt;">Ran
Friedman wrote:
<blockquote type="cite"> Hi,<br>
<br>
The numerical derivative for the Nth value y[N] is calculated as:<br>
der = y[N+1] - y[N-1] * 0.5 * deltaX<br>
</blockquote>
Correction:<br>
der = (y[N+1] - y[N-1]) * 0.5 * deltaX
<blockquote type="cite">where y
is the potential deltaX is the difference between two
successive values in your input (e.g., 1 if you have a table that goes
from -180 to 180 with 361 values).<br>
<br>
I don't think you can print the number without changing the code, but
it's not difficult to calculate. You can plot your forces and -der and
see where they deviate. <br>
<br>
Ran.<br>
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