**From:** Faramarz Joodaki (*fjoodaki_at_my.uri.edu*)

**Date:** Fri Jul 07 2017 - 18:04:48 CDT

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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

**Next message:**Jérôme Hénin: "Re: ABF FEP with multichain receptor"**Previous message:**yousef nademi: "Re: Lipid_bilayer_area_per_lipid_problem_using_NPT_CharmmForcefield"**Next in thread:**Faramarz Joodaki: "Re: Cross-term (CMAP)"**Reply:**Faramarz Joodaki: "Re: Cross-term (CMAP)"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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