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

[shahid nayeem]

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> 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
>>
>
> --
> ========================================
>
> 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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