[AMBER] Simulating dehydrated bilayers with a vacuum above and below

From: Blake Armstrong <blake.armstrong.student.curtin.edu.au>
Date: Fri, 23 Jul 2021 07:50:52 +0000

Hi AMBER users,

I am trying to simulate a 128-DOPC lipid bilayer at dehydration levels of ~5 water molecules per lipid. However, it has been reported that interactions between the periodic images in the z-direction can cause issues in the simulations. According to this paper: https://pubs.acs.org/doi/full/10.1021/la100891x the Gromacs software has been able to separately couple pressure to the x and y directions and fix the z component of the unit cell to leave a void space of vacuum above and below the membrane. I've tried to replicate this in Amber20, but I've only found the 'baroscalingdir' option which allows two directions to be fixed, but not one. Is there some other way I can achieve this within Amber?


Blake Armstrong
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Received on Fri Jul 23 2021 - 01:00:02 PDT
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