[AMBER] read the traj file to analyzing hbonds

From: Ehsan Habibi <EHabibi.ibb.ut.ac.ir>
Date: Sun, 05 Sep 2010 22:17:47 +0430

Dear Amber users,
the following is the information of md2:
imin = 0, irest = 1, ntx = 7,
   ntb = 2, pres0 = 1.0, ntp = 1,
   taup = 2.0,
   cut = 9.0, ntr = 0,
   ntc = 2, ntf = 2,
   tempi = 303.0, temp0 = 303.0,
   ntt = 3, gamma_ln = 1.0,
   nstlim = 50000, dt = 0.001,
   ntpr = 100, ntwx = 100, ntwr = 100
 /

How can I calculate the number of snapshots for analyzing the hbonds with
ptraj?
trajin model_wat_md2.mdcrd 1 10000 1
is it mean:
1: Read in the trajectory file starting at 1 to 50000
10000: give me 10000 snapshots
1: consider each one

Thank you so much in advanceRegards,
Ehsan
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Received on Sun Sep 05 2010 - 11:00:03 PDT
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