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
similar)?
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.
-Justin
some basic mistakes . Any suggestion and help will highly appreciated.
Thanking you in advance.
msnayeem
msnay...@gmail.com
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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