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 <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <gmx-users@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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <gmx-users@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: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED])
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: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED])
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
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