[gmx-users] Visualization of .trr problem in VMD

Justin A. Lemkul jalemkul at vt.edu
Sat Apr 3 14:48:38 CEST 2010

shahid nayeem wrote:
> Dear All
> I am working on protein unfolding
> simulation in gromacs. when I do a production run on 32 node HPC I get
> .trr  file along with .gro. when I try to visualize this files in
> VMD I see erratic large movement of atoms in the trajectory. With same
> .mdp files when I did smaller run of 2ns on single PC and viewed .trr
> and .gro in VMD, the movemnt of atom was smooth. Why this is
> happening. When I used the command g_filter to produce lowpass.xtc

This sounds like a consequence of periodic boundary conditions.  Have you tried 
using trjconv to fix the PBC effects (i.e., -pbc mol, -pbc nojump, or something 

> with -nf 10 I got the smooth movement of atoms. Is it always essential
> to use g_filter with .trr file of HPC multinode output. what is the
> difference between lowpass.xtc and highpass.xtc. For the pupose of

The purpose is to smooth out high-frequency vibration to make visualization a 
bit easier and movie-rendering more meaningful.  See g_filter -h for the 
difference between the two; they are explained quite thoroughly.

> RMSD calculation should I use the output of g_filter i.e. lowpass.xtc
> or the original .trr file. I am new in this field so excuse me for

Use the original (PBC-corrected) trajectory.


> some basic mistakes . Any suggestion and help will highly appreciated.
> Thanking you in advance.
> msnayeem
> msnayeem at gmail.com


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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