AMBER Archive (2007)

Subject: AMBER: distcovar in ptraj

From: Zhenyu Lu (biosimu_at_yahoo.com)
Date: Mon Mar 26 2007 - 22:00:13 CST

Hi, for "distcovar" calculations with ptraj, the code in actions.c calculates the matrix element for pairs ij, kl, with the condition k>=i, and l >=max(k+1,j). But does this skip those matrix elements satisfying j>k>i, k+1<l<j?

or should the code be changed from
> atcnt4 = (k>=j ? atcnt3+1 : atcnt2);

> for(l=(k>=j ? k+1 : j); l < action->state->atoms; l++){
to
< atcnt4 = (atcnt3==atcnt1 ? atcnt2 : atcnt3+1);
< for(l=(k==i ? j : k+1); l < action->state->atoms; l++){ 

---

Thanks!

Zhenyu

 
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