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

From: James W. Snyder, Jr. <>
Date: Wed, 20 Nov 2013 16:33:46 -0800 (PST)


I'm using using a weak harmonic restraining potential (water cap) to keep the water inside a sphere of radius 45A, so water diffusion is not a problem. However, I think my problems are almost certainly related to neglecting large portions of the electrostatic interactions. So, it seems like I can do one of two things. I can increases cut to 9999.9 or I can do a period simulation. I'll probably do a periodic simulation because it will be much faster, so it will solve both problems that I'm having. I'm using spcf water by the way.



----- Original Message -----
From: "Daniel Roe" <>
To: "AMBER Mailing List" <>
Sent: Wednesday, November 20, 2013 2:35:27 PM
Subject: Re: [AMBER] Nudged Elastic Band with Explicit Solvent for a Larger Protein


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)
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Received on Wed Nov 20 2013 - 17:00:02 PST
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