>From section 6.2 of the AmberTools manual:
trajin filename [ start stop offset] [remdtraj remdtrajtemp reptemp]
So 'trajin model_wat_md2.mdcrd 1 10000 1' means read
model_wat_md2.mdcrd starting at frame 1 and ending at frame 10000 with
an offset of 1 (i.e. read each one). It sounds like what you want is
'trajin model_wat_md2.mdcrd 1 50000 5'. This will start reading at
frame 1 and end at frame 50000; the offset of 5 tells ptraj to skip
every 5 frames so you should end up with 10000 snapshots.
Hope this helps.
-Dan
On Sun, Sep 5, 2010 at 1:47 PM, Ehsan Habibi <EHabibi.ibb.ut.ac.ir> wrote:
> 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 Mon Sep 06 2010 - 06:30:03 PDT
