[gmx-users] trjconv output at a specified time

[Alan Dodd]

Select a group: 2
Selected 2: 'Protein-H'
trn version: GMX_trn_file (single precision)
Reading frame       0 time  125.000

'nuff said.  Couldn't comment on the time between frames in your file.  gmxdump will tell you, or get it from (nstxout or nstxtcout)*dt in your mdp.



----- 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 11:24:00 PM
Subject: Re: [gmx-users] trjconv output at a specified time

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
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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