Re: [AMBER] POPC membrane separation.

From: Jason Swails <>
Date: Thu, 29 Jan 2015 08:49:42 -0500

On Thu, 2015-01-29 at 12:32 +0000, William Hester wrote:
> Hi Ross,
> You are correct, the minimisation/ heating was run at NVT and then NPT
> for the MD. I am inexperienced in biological simulations and haven’t
> heard of formation vacuum bubbles before. Is there any specific reason
> for this, during the building of the system for example?

Yes :). If you hold the volume fixed, and that volume is too large,
then the external pressure that leads to those conditions must be *very*
low. Basically, your simulation is boiling.

> I specified the PBC by opening the system in VMD and using the
> minimax measurement which makes me wonder if the membrane wasn’t
> sufficiently tightly around the protein?

minmax overestimates the box size. Not horribly, but it does. NPT is
really the best way to get the "correct" box size for standard
> I checked the XST file during the MD and sure enough the cell
> dimensions converge to a value of about 5A less in each direction so I
> have restarted the simulations and no separations! Thank you so much
> for the help - I’ve been stuck on this for a couple of weeks now!


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Jan 29 2015 - 06:00:02 PST
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