[gmx-users] gmxcheck and trjconv

[spitaleri.andrea at hsr.it]

Hi Tsjerk,
true!!!! 
i have to remember to start to count from 0 ... as usual :P

thanks 

andrea

Andrea Spitaleri PhD
Dulbecco Telethon Institute 
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)

----- Original Message -----
From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
Date: Wednesday, March 7, 2007 5:56 pm
Subject: Re: [gmx-users] gmxcheck and trjconv

> Hey Andrea,
> 
> Also note that you have 70 FRAMES with 1 ps time step. That means,
> with the first frame at t=0, that you have a maximum time of (70-1)*1
> ps = 69 ps in the output.
> 
> Ciao!
> 
> Tsjerk
> 
> On 3/7/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> > andrea spitaleri wrote:
> > > Hi,
> > > however in md0.log the right time is reported (69 and not 70)
> > >
> > > and
> > >
> > > David van der Spoel wrote:
> > >> andrea spitaleri wrote:
> > >>> Hi all,
> > >>> silly question. I have checked a trr with gmxcheck and I get 
> this> >>> output below:
> > >>> Item        #frames Timestep (ps)
> > >>> Step            70    1
> > >>> Time            70    1
> > >>> Lambda          70    1
> > >>> Coords          70    1
> > >>> Velocities      24    3
> > >>> Forces           0
> > >>> Box             70    1
> > >>>
> > >>> however if then i use trjconv to dump a configuration file 
> at 70 ps it
> > >>> says:
> > >>> WARNING no output, trajectory ended at 69
> > >>>
> > >>> Is it normal? I don't mind to extract a configuration file 
> at 69 ps,
> > >>> however i was wondering if this
> > >>> behaviour is normal or whether it is bug.
> > >>>
> > >>> thanks in advance
> > >>>
> > >>> Regards
> > >>>
> > >>> andrea
> > >> is the simulation still running? then file buffering may play 
> in. alt.
> > >> if you kill -9 then the buffers will not be flushed.
> > >>
> > >
> > buffering is separate per file. in trr you have only half a frame.
> >
> > --
> > David.
> > 
>
________________________________________________________________________>
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,          75124 Uppsala, Sweden
> > phone:  46 18 471 4205          fax: 46 18 511 755
> > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
> > 
>
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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
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