[gmx-users] trjconv output at a specified time

[Liu Shiyong]

Thanks.

The trajectory starts at 125ps ?

So  step 1  == 125 ps
      step 2 ==   250 ps
      step 3  ==  375 ps

Where is 125ps from ?

But

; RUN CONTROL PARAMETERS
integrator               = steep
; Start time and timestep in ps
tinit                    = 0
dt                       = 0.002



On Wed, Mar 12, 2008 at 5:32 PM, Alan Dodd <anoddlad at yahoo.com> wrote:

> You asked for the frame at 1ps.  The trajectory starts at 125ps, so
> unsurprisingly the program does not give you an output.
>
> ----- Original Message ----
> From: Liu Shiyong <liushiyong at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Wednesday, March 12, 2008 10:07:17 PM
> Subject: [gmx-users] trjconv output at a specified time
>
> Hi,
>
> I want to output a structure in a given time, for example , in step 1
> during minimization.
>
> I tried the following command using dump:
> trjconv -f r-l_1_oplsaa.minim_traj.trr -timestep 1 -o m.pdb  -s
> r-l_1_oplsaa.input.tpr  -t0 0 -dump 1
>
> But It didnot work.
>
> Output msg:
>
> Select a group: 2
> Selected 2: 'Protein-H'
> trn version: GMX_trn_file (single precision)
> Reading frame       0 time  125.000
> Back Off! I just backed up m.pdb to ./#m.pdb.1#
> Last frame         19 time 2418.000
>
> WARNING no output, trajectory ended at 2418
>
>
> gcq#76: "Baseball Heroes Only" (P.J. Harvey)
>
> Best
>
> --
> Shiyong Liu
> Research Assistant
> center for bioinformatics in the university of kansas
> Lab: (785)864-1962
> Email: syliu at ku.edu (shiyongliu at ku.edu or liushiyong at ku.edu)
> Homepage: http://www.people.ku.edu/~syliu<http://www.people.ku.edu/%7Esyliu>
> Lab: http://vakser.bioinformatics.ku.edu/people
> Phone: (785) 864-1962
>
>
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-- 
Shiyong Liu
Research Assistant
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: syliu at ku.edu (shiyongliu at ku.edu or liushiyong at ku.edu)
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
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