[gmx-users] Time unit issue with g_anaeig
kei.sit at qut.edu.au
Tue Nov 15 00:19:32 CET 2011
I ran gmxcheck and it returned the following output:
Checking file 1-21.trr
trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
# Atoms 7764
Reading frame 49000 time 4900.000
Item #frames Timestep (ps)
Step 49984 0.1
Time 49984 0.1
Lambda 49984 0.1
Coords 49984 0.1
Box 49984 0.1
I understand now why the time is 10 times smaller in my analysis, but this now raises another question as to why it is 0.1ps per frame. Would it have something to do with the converting from a DCD format to a TRR format? I just checked the configuration file for my MD run and I can still see that I'm running the simulation of 2fs timesteps and saving output every 500 steps which should equate to 1ps. Once again, thank you for your time in helping.
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham
Sent: Monday, 14 November 2011 6:47 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Time unit issue with g_anaeig
On 14/11/2011 5:46 PM, Kei Sit wrote:
I'm new to gromacs so I hope I haven't done something wrong that is extremely simple. I have recently been using gromacs to analyse an MD trajectory using g_covar and g_anaeig. I have output saved to the trajectory every ps and I currently have a trajectory with 49000 frames (49ns).
I initiate g_anaeig with this command:
g_anaeig -v eigenvec.trr -f 1-21.trr -s protein.pdb -eig eigenval.xvg -proj projection.xvg -xvgr -first 1 -last 8
While this is being executed I see this:
Reading frame 1000 time 100.00
which continues increasing as more frames are read.
When I go to visualise projection.xvg, the time scale is in ps (natural as the default value is in ps) but it only shows 4900ps and not 49000ps.
My issue is this, why is the time constantly 10 times smaller than the number of frames that are being read? Am I not entering something correctly which fixes this?
What does gmxcheck have to say about your trajectory files?
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