Dear David and all,
This seems like a very large number of frames and thus bring some questions
to mind.
At present I have 2000 frames for a 40 ns simulation, thus what would you
recommend?
To decrease the ntwx from the current 10000 to maybe 100. This would give
200,000 frames (and a huge traj file ~ 100 GB).
Or run a longer MD simulation (e.g. 100 ns) and keep ntwx=100 to get
500,000 frames and > 200 GB file.
How does the calculation scale with such larger traj files? For 2000
frames it took 2.195 hr.
I got the following numbers after analyzing 2, 200, 400 and all 2000 frames
from the current 40 ns traj.
From this data, can one expect/predict that having a very large number of
frames (as you suggested) will decrease the total DS to realistic values?
In the tutorial for nmode (here
<
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section5.htm>)
it is mentioned that temperature is included in the reported DS value, but
such info is not clear from the output for quasi-harmonic calculation.
Also, it will be helpful if you can suggest how to troubleshoot the mode
calculation especially in the absence of useful error messages.
Looking forward to your valuable suggestions on these aspects.
thank you and best regards.
translational rotational vibrational total # frames
DELTA S: -15.5315 -14.8932 -2.9448 -33.3695 2.00
DELTA S: -15.5315 -14.8717 -369.095 -399.498 200.00
DELTA S: -15.5315 -14.8708 -593.121 -623.524 400.00
DELTA S: -15.5315 -14.8696 -733.876 -764.277 2000.00
On Tue, Apr 20, 2021 at 12:09 AM David A Case <david.case.rutgers.edu>
wrote:
> On Mon, Apr 19, 2021, Vaibhav Dixit wrote:
>
> >I have a total of 2000 frames in the trajectory.
> >How many would you consider sufficient for this type of complex with a
> >total of 234 residues?
>
> You need a minimum of 3N frames to get a complete quasiharmonic calculation
> of a system with N atoms. Since you have about 40,000 atoms, you would
> need
> at least 120,000 frames (and realistically, many times this number) in
> order
> to carry out a quasiharmonic analysis.
>
> ....dac
>
>
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--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
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Received on Tue Apr 20 2021 - 00:30:02 PDT
