Re: [AMBER] low-water system, bad NPT and NVT

From: Carlos Simmerling <>
Date: Mon, 17 Jan 2022 19:38:29 -0500

Solvating with methods like solvatebox tends to leave the density too low,
and I can imagine that your system is to compress. But depending on ions
etc there might be a lot of repulsion. It could be worth thinking about
making a bigger system to start, maybe restraining the DNA and letting
water work in. Methods like MC water moves might help too (

On Mon, Jan 17, 2022, 6:01 PM Daniel Konstantinovsky <> wrote:

> Dear Amber,
> I am trying to run a simulation of a system of nine DNA molecules closely
> packed into a 3x3 grid. To solvate the system without increasing the size
> of the box much I have been trying
> solvatebox mol TIP4PBOX 0.0
> which has been working fine. The system seems to do energy minimization
> fine as well. The problem starts when I try to run dynamics. First of all,
> NVT dynamics with pmemd.cuda become *extremely* slow (4 ns / day instead of
> 50-100 for a system this big). Second of all, any NPT simulation fails
> immediately because the box size decreases too fast. I need to coax this
> system into a smaller box to get rid of waters on the edges of the 3x3 DNA
> grid before I increase the z-dimension of the box and simulate the system
> as a vacuum-water interface. If I don't do NPT first, the system starts
> "leaking" and expanding into the empty spaces the original box provides.
> How can I solve these problems?
> Thank you!
> Dan
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Received on Mon Jan 17 2022 - 17:00:01 PST
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