Dear Amber experts,
I recently ran a test entropy calculation on a single frame of a MD
trajectory to obtain an nmode calculation result and an estimation of
the necessary computational resources; however, after the standard nmode
calculation, a second entropy calculation method (quasiharmonic), which
obtains the entropy from the trajectory analysis, seems to be triggered
automatically!
In the Amber 23 manual (section 38.3.1) I could not find any clear
description of selecting the methods within the &nmode input section;
the MMPBSA.py introduction (section 38.1) just states that two entropy
calculation methods are available.
How can I select either or both of the entropy calculation methods?
(Can the computation time for the quasiharmonic analysis roughly be
guessed from the time necessary for a single nmode calculation?)
I included the MMPBSA output (calculation still running) and my input
file at the end of this e-mail.
Any help is appreciated!
Best regards,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
------- STDOUT from the MMPBSA.py run
Loading and checking parameter files for compatibility...
cpptraj found! Using /data1/soft/amber22at23/bin/cpptraj
mmpbsa_py_nabnmode found! Using
/data1/soft/amber22at23/bin/mmpbsa_py_nabnmode
Preparing trajectories for simulation...
502 frames were processed by cpptraj for use in calculation.
1 frames were processed by cpptraj for nmode calculations.
Running calculations on normal system...
Beginning nmode calculations with
/data1/soft/amber22at23/bin/mmpbsa_py_nabnmode
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning quasi-harmonic calculations with
/data1/soft/amber22at23/bin/cpptraj
------- Input file for the MMPBSA.py run
# MMGBSA input / interaction energy
&general
verbose=2,
keep_files=1,
netcdf=1,
entropy=1,
/
&nmode
nmstartframe=1,
nmendframe=1,
nmode_igb=1,
nmode_istrng=0.0,
/
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Received on Mon Feb 19 2024 - 02:00:02 PST
