[AMBER] inquiry regarding minimum-image convention in cpptraj

From: Akshay Prabhakant <akshayresearch16.gmail.com>
Date: Mon, 24 Feb 2020 00:43:03 +0530

Respected Amber Community,
Our group is trying to calculate the linear interaction energy(lie) between
two groups of atoms, from our MD trajectories. We ran the MD using PBC, but
it seems that while running LIE(the tool from CPPTRAJ), it does not seem to
have used the PBC while calculating the VDW/EELEC energies . Does the
cpptraj tool in AMBER use the minimum-image convention(i.e. the periodic
boundary conditions)? If yes, should any arguments be specified/ command
needed to be run? If no, then how can we generate potential energy between
2 masks using PBC, for a given .nc trajectory file?

Thanking in advance,
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Received on Sun Feb 23 2020 - 11:30:02 PST
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