Cross-term (CMAP)

From: Faramarz Joodaki (fjoodaki_at_my.uri.edu)
Date: Fri Jul 07 2017 - 18:04:48 CDT

Hi everyone!

I have a question about the cross-term in NAMD source code. From the source
code, file "ComputeCrossterms.C", I found that NAMD is using bicubic spline
interpolation to find the energy and first derivative of cross-term energy
respect to Phi and Psi.

As I found:

dU/d(phi) is
fx += dxa[i] * ya[j] * table[ij].d00
        + dxb[i] * ya[j] * table[ij].d10
        + dxa[i] * yb[j] * table[ij].d01
        + dxb[i] * yb[j] * table[ij].d11;

and dU/d(psi) is
 fy += xa[i] * dya[j] * table[ij].d00
        + xb[i] * dya[j] * table[ij].d10
        + xa[i] * dyb[j] * table[ij].d01
        + xb[i] * dyb[j] * table[ij].d11;

I would like to calculate the second derivative respect to Phi and Psi.
According to these formulae, for example, I am using to use below formula
for d2U/d(Psi)2

fyy += xa[i] * d2ya[j] * table[ij].d00
          + xb[i] * d2ya[j] * table[ij].d10
          + xa[i] * d2yb[j] * table[ij].d01
          + xb[i] * d2yb[j] * table[ij].d11;

I would be so grateful if you could guide is the way of my thought is
correct?

Best Regards,
Faramarz

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:25 CST