In the future, please start a new thread if you're moving on to a new topic.
The Berendsen algorithm does not sample from any known statistical mechanical
ensemble. The kinetic energy itself is calculated correctly, but the
distribution of these values is not related to any rigorous ensemble. If you're
concerned about the legitimacy of using Berendsen, then go ahead and use a more
reliable method like Nose-Hoover.
-Justin
shahid nayeem wrote:
Thanks alot I did solve visualization problem using trjconv. Is it o.k.
to use Berendsen thermostat for thermal unfolding of protein. I came
across literature saying Berendsen coupling does not gives accurate
kinetic Energy. I am using it and I am getting my protein unfolded. Am I
right. Can I use the trajectory obtained for thermodynamic analysis.
Thanks in advance
msnayeem
On 4/3/10, *Justin A. Lemkul* <[email protected] <mailto:[email protected]>>
wrote:
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
[email protected] <mailto:[email protected]>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
========================================
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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