[gmx-users] trjconv output at a specified time

Alan Dodd anoddlad at yahoo.com
Wed Mar 12 23:32:28 CET 2008

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


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)


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

-----Inline Attachment Follows-----

gmx-users mailing list    gmx-users at gromacs.org
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080312/10fb9ba7/attachment.html>

More information about the gromacs.org_gmx-users mailing list