Dear Dan,
If I write:
'trajin model_wat_md2.mdcrd" without [ start stop offset], Does it mean "
read all the trajectory file"?
because when I mention any [strart stop offset] (e.g. 1 50000 5) I give me
500 set:
PTRAJ: trajin creb_wat_md2.mdcrd 1 50000 5
Checking coordinates: creb_wat_md2.mdcrd
FYI ptrajSetupIO(): trajin stop value (50000) is greater than the number of
sets read in.
Setting stop to the maximum value (500)
PTRAJ: trajout creb_nowat_md2.mdcrd
PTRAJ: center :1-110
Mask [:1-110] represents 1950 atoms
PTRAJ: strip :WAT
Mask [:WAT] represents 48075 atoms
PTRAJ: strip :Cl-
Mask [:Cl-] represents 16 atoms
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 100 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (creb_wat_md2.mdcrd) is an AMBER trajectory (with box info) with 500
sets (processing only 100)
OUTPUT COORDINATE FILE
File (creb_nowat_md2.mdcrd) is an AMBER trajectory (with box info)
ACTIONS
1> CENTER to box center via center of geometry, atom selection follows
:1-110
7> STRIP: 48075 atoms will be removed from trajectory: :127-16151
7> STRIP: 16 atoms will be removed from trajectory: :111-126
Processing AMBER trajectory file creb_wat_md2.mdcrd
Set 1 . . . . . . . . . .
Set 50 . . . . . . . . . .
Set 100 . . . . . . . . . .
Set 150 . . . . . . . . . .
Set 200 . . . . . . . . . .
Set 250 . . . . . . . . . .
Set 300 . . . . . . . . . .
Set 350 . . . . . . . . . .
Set 400 . . . . . . . . . .
Set 450 . . . . . . . . . .
Set 500
PTRAJ: Successfully read in 500 sets and processed 100 sets.
Dumping accumulated results (if any)
Regards,
Ehsan
-----Original Message-----
From: Daniel Roe <daniel.r.roe.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Date: Mon, 6 Sep 2010 09:06:33 -0400
Subject: Re: [AMBER] read the traj file to analyzing hbonds
>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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> AMBER.ambermd.org
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Received on Mon Sep 06 2010 - 07:30:04 PDT
