Re: [AMBER] Symmetrical voids during heating stage

From: Thomas Cheatham <>
Date: Thu, 7 Oct 2021 03:48:50 +0000

In equilibration during the MD phases, you need constant pressure

   ntb=2, ntp=1

LeAP by default is a little under density for water (by default), so if you do MD in constant volume (post min), vacuum bubbles will form. You can overcome this a bit by setting closeness 0.98 with solvateoct... Just reminds me we need to fix these things and setup better tutorials which we are trying to do (but I've said this for multiple years, so my bad). I'll try to follow through. Of course, once you turn on constant pressure, the restraints become an issue due to scaling molecules (and restraint coordinates). If issues, e-mail me directly; problems we faced for a long time, we have work arounds in our labs, yet we did not fully "automate". MD is not a black box, or at least we haven't fully black boxed it (meaning fully automated the workflows).


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Received on Wed Oct 06 2021 - 21:00:02 PDT
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