AMBER Archive (2008)

Subject: AMBER: time autocorrelation: ??

From: fatima.chami_at_durham.ac.uk
Date: Mon Feb 04 2008 - 12:05:47 CST

Dear Amber's users,

I am using the following command to calculate the time autocorrelation
function (using ptraj) but it did not work!

vector v1 :1_at_C13,:1_at_C15,:1_at_C36 corrplane order 2
analyse timecorr vec1 v1 vec2 v1 tstep 2 norm out v1_plane.out

i also tried it with:
vector v1 :1_at_C13,C15,C36 corrplane order 2

the output shows:
PTRAJ: vector v1 :1_at_C13, :1_at_C15, :1_at_C36 corrplane order 2
Mask [:1_at_C13,] represents 1 atoms
WARNING in ptraj(), vector: < 3 atoms given for vector corrplane, ignoring command

PTRAJ: analyse timecorr vec1 v1 vec2 v1 tstep 2 norm out v1_plane.out
WARNING in ptraj(), analyze timecorr: no vector with name v1 found, ignoring command
[No output trajectory specified (trajout)]

any help

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