[AMBER] Speed-up calculation of Entropy with MMPBSA

From: James Starlight <jmsstarlight.gmail.com>
Date: Mon, 18 Feb 2019 10:34:22 +0100

Dear Amber users,

I am performing MMGBSA post-processing of Amber trajectory for water
soluble protein of ~ 200 residues bound to sugar ligand. For the 100
ns trajectory, I take only 200 snapshots, e.g:
startframe= 1, interval=5, entropy=1, keep_files=2,
strip_mask=:WAT:Cl-:NA+:K+, netcdf=1
igb=5, saltcon=0.150,

nmstartframe=1, nminterval=1, nmode_igb=1, drms=0.05, nmode_istrng=0.15,

Using 8 cpus of the local CPU machine I have very fast calculation of
enthalpy contribution but on the stage of entrophy calculation (via
NMA or harmonic approximation) the calculations are stuck. Could you
suggest me something to improve performance of the calculations? Would
it be possible to use less interval with NMA for calculations of
enthropy with NMA?

thanks in advance!

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Received on Mon Feb 18 2019 - 02:00:02 PST
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