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

From: Daniel Konstantinovsky <daniel.konstantinovsky.yale.edu>
Date: Mon, 17 Jan 2022 18:01:09 -0500

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!
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Received on Mon Jan 17 2022 - 15:30:02 PST
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