[gmx-users] Time unit issue with g_anaeig

Kei Sit kei.sit at qut.edu.au
Tue Nov 15 00:26:05 CET 2011

Hi again,

I just found the solution to the problem. Using trjconv to specify the timestep seems to have helped. Thanks again for the help.


From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Kei Sit
Sent: Tuesday, 15 November 2011 9:20 AM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] Time unit issue with g_anaeig

Hi Mark,

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
Velocities       0
Forces           0
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:
Hi all,

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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