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

shahid nayeem msnayeem at gmail.com
Sat Apr 3 13:07:42 CEST 2010

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
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
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
some basic mistakes . Any suggestion and help will highly appreciated.
Thanking you in advance.

msnayeem at gmail.com

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