[AMBER] Lateral diffusion of lipid head groups

From: Maria Bzówka <m.bzowka.tunnelinggroup.pl>
Date: Thu, 15 Aug 2019 13:12:21 +0200

Hi All,

Recently I was reading the discussion about calculating the diffusion
coefficient (from Amber manual), but I would like to ask some additional
questions. If I want to calculate the lateral diffusion of lipid head
groups in the xy dimension, should I use stfcdiffusion command in cpptraj
instead of diffusion command? If I understand correctly, with stfcdiffusion
command as an output I'll get MSD vs. time, but then I need to proceed
further with the results, right? On the other hand, using the diffusion
command would give me the diffusion constant immediately but not in xy

Thank you in advance for the explanation

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Received on Thu Aug 15 2019 - 04:30:03 PDT
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