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

[Justin A. Lemkul]

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* <jalemkul at vt.edu <mailto:jalemkul at vt.edu>> 
> 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
> 
>         msnayeem at gmail.com <mailto:msnayeem at 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 <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

========================================