[AMBER] Creating a coarse-grained trajectory from an all atomistic simulation

From: SARAH JEANNE LEFAVE <s.lefave.utah.edu>
Date: Wed, 23 Jan 2019 15:22:01 +0000

Hi all,

Is it possible to essentially create a coarse-grain trajectory, using coordinates of either each residues center of mass or the alpha carbon position, from an all atomistic trajectory? I have experimented with the ‘vector’ command in cpptraj, but have only been able to get the center of mass coordinate for either 1 residue or the entire protein. I think I could possibly output the coordinates of each residue individually and concatenate them later, but this would be difficult to get over many frames and also in a larger protein system I’m not sure that’s a realistic option.

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Received on Wed Jan 23 2019 - 07:30:02 PST
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