[AMBER] Lipid diffusion COM drift

From: Christopher Faulkner <FaulknerC3.cardiff.ac.uk>
Date: Fri, 22 Jun 2018 08:43:22 +0000

Dear Amber users,

I am having some trouble in the correction of COM drift in my lipid system so I can calculate diffusion coefficients.

I have found the movement of the upper monolayer COM using the cpptraj commands:

trajin bilayer_run.nc

vector com center out upper_movement.dat :1-192


I have created the new prmtop and trajectory of the upper monolayer only:

parm DOPC.prmtop
trajin DOPC.nc
strip !(:1-192) outprefix upper

trajout DOPCupper.nc

I am unsure about how to reset the monolayer by the corresponding movement (in X, Y, Z) to create a new trajectory without monolayer COM drift.

Any help is appreciated,

Christopher Faulkner

PhD student

Cardiff University
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Received on Fri Jun 22 2018 - 02:00:02 PDT
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