Dear All
I run 1ns simulation with 1040 frame for a protein which consists of 388 residues. so I have 1040 snapshot. For ptraj:
trajin file1.crd
distance a1 out file2.dat time 1 : 1: 388
strip :WAT
go
I just would like to know that when we go to see the contact we need to consider the contact of residue 1 with 377 other residues, if I m not mistaken, a matrix of 388*387/2. Is there any possiblities to calculate all contact at one time. thanks for your participation.
Regards
Rose
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Received on Wed Mar 07 2007 - 06:07:19 PST
