Re: The reason for the formation of bubbles in heating stage

From: Danilo Di Maio (
Date: Mon Jan 09 2017 - 09:09:58 CST

That happened to me several times when I prepared a system with AmberTools. Basically in that case I had this problem because I guess Ambertools adds waters with an incorrect density (lower than that at room temp). This means that you have less waters than you should have at room temp for a box of a given volume. This ultimately leads to the fact that when you heat a constant volume, waters redistribute within the box to the "correct" room temp density and, since at the beginning you have added too few waters than you should have done , you end up with having a void. This void has the form of a bubble to minimize surface tension, I suppose.

Anyway solving this problem should be very easy, just do a very short (100-200ps) equilibration in NPT (with all protein atoms restrained) in order to readjust box volume before heating and you should be fine!


Il giorno 09/gen/2017, alle ore 15:16, Mohaddeseh Habibzadeh <> ha scritto:

> ​Hi all
> I heated up the system (nvt) to 310 kelvin slowly, but in 200 k I saw the bubbles in the box.
> What is the reason for the formation of bubbles in heating stage?
> Sincerely

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