Re: [AMBER] Nudged Elastic Band with Explicit Solvent for a Larger Protein

From: Daniel Roe <>
Date: Wed, 20 Nov 2013 15:35:27 -0700


On Wed, Nov 20, 2013 at 2:34 PM, James W. Snyder, Jr.
<> wrote:
> I'm using ntb=0 because I need to eventually use Amber/TeraChem to do QM/MM on the system, and I can't use periodic boundary conditions. I

Even if you eventually don't need PBC you certainly need them if
you're doing an explicit solvent MD simulation of any kind, otherwise
your water at the edges of your system is free to diffuse where it
will. Also, you're neglecting large portions of your electrostatic
interactions if you have ntb=0 and a cutoff that is smaller than your
system (with PBC these are handled by the reciprocal part of the PME
calculation). You can always remove the water and box information from
your system later on if you need to, using e.g. cpptraj.

> probably do not need to use jfastw=4 though, but I was using this because there are some crystallization waters that interact with the protein,
> and I didn't want to use TIP3P water.

Which water model are you using?

> But, these interactions are not very important for NEB. Do you think I should run this simulation
> with cut = 9999.9 and fast water, or is it a bad idea to run NEB with explicit water? Minimization with cut < 9999.9 seems to be problematic
> for getting well minimized structures.

Depending on your system, running NEB in explicit solvent might be the
only good solution, e.g. when simulating nucleic acids, see Just run your
minimization/MD with PBC and you should see improved behavior.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
AMBER mailing list
Received on Wed Nov 20 2013 - 15:00:02 PST
Custom Search