[gmx-users] Trjconv: reducing frames and Time issue

[Tsjerk Wassenaar]

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 <anoddlad at yahoo.com> wrote:
> Don't use -timestep.  Just -skip will do for what you want.
>
> ----- Original Message ----
> From: "bmmothan at ucalgary.ca" <bmmothan at ucalgary.ca>
> To: gmx-users at 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