Hi,
What Alan refers to is the following:
-timestep time 0 Change time step between input frames (ps)
which you could have read from the manual/manpage/help on trjconv.
With timestep you change the time step between the frames (to 20ps),
skipping 2 frames, makes 40ps timesteps in your output frame, and half
the frames. Sounds to me that you got what you bargained for.
Tsjerk
On 5/8/07, Alan Dodd <[EMAIL PROTECTED]> wrote:
Don't use -timestep. Just -skip will do for what you want.
----- Original Message ----
From: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Tuesday, May 8, 2007 7:20:39 PM
Subject: [gmx-users] Trjconv: reducing frames and Time issue
Hello All,
I have a xtc file and I used trjconv on it to reduce the number of frames
using:
trjconv -f original.xtc -o reduced-frames.xtc -s xx.tpr -timestep 20 -fit
rot+trans -skip 2 -center no
Now I have two xtc files for a 10ns simulation:
original.xtc
reduced-frames.xtc
I did gmxcheck to check the number of frames and time (I will show the
results for both below). The problem is: the number of frames is reduced
by half however the time shown on the reducedframes.xtc is increased!!
(from 10 000 ps to 100 000 ps).. I cant understand what this means? I did
a g-cluster analysis and they r saying I did a 100 000ps simulation which
it not true! can anyone explain this to me?
original.xtc
Reading frame 0 time 0.000
# Atoms 5100
Precision 0.001 (nm)
Last frame 5000 time 10000.000
Item #frames Timestep (ps)
Step 5001 2
Time 5001 2
Lambda 0
Coords 5001 2
Velocities 0
Forces 0
Box 5001 2
reduced-frames.xtc
Reading frame 0 time 0.000
# Atoms 92
Precision 0.001 (nm)
Last frame 2500 time 100000.000
Item #frames Timestep (ps)
Step 2501 40
Time 2501 40
Lambda 0
Coords 2501 40
Velocities 0
Forces 0
Box 2501 40
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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