Re: [AMBER] NVE Energy/Temperature Drift Issue

From: James W. Snyder, Jr. <>
Date: Mon, 1 Jul 2013 21:40:05 -0700 (PDT)


Yeah, so I am not totally sure how much the energy is drifting because there is a lot of noise. The temperature drifts by 60K is 120ps roughly. Also, I am using an explicit solvent model/solvation sphere. From what I understood, this warranted using ntb=0 and igb=0. If that's not the case, please let me know. Also, I don't really want to write the results every step. Those comments are residual from when I was debugging something. I think dsum_tol = 0.000001 is also from something else, but I didn't bother removing it because it has no impact on the calculation.



----- Original Message -----
From: "Daniel Roe" <>
To: "AMBER Mailing List" <>
Sent: Monday, July 1, 2013 9:17:59 PM
Subject: Re: [AMBER] NVE Energy/Temperature Drift Issue


Could you provide some more details? Could you quantify what you mean
by substantial drift? The options ntb = 0 and since it's not
explicitly set igb = 0 imply you're running your calculation in vacuum
- is that correct? If so, your cutoff (16.0) seems really low,
especially for a 25K atom system - also note that Amber force fields
were not designed with vacuum calculations in mind, so you should be
cautious in interpreting your results.

On Mon, Jul 1, 2013 at 9:35 PM, James W. Snyder, Jr.
<> wrote:
> ntpr = 1000, !print detials to log every step
> ntwx = 1000, !write coordinates to mdcrd every step
> ntwr = 1000, !write restart file every step

If you really want to be writing this stuff every step (as your
comments imply) these should be set to 1, although that's really only
useful for debugging purposes.

> dsum_tol = 0.000001, ! Increase PME accuracy

Since you're not using the PME code (ntb = 0) this option has no effect.


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) 585-9119 (Fax)
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Received on Mon Jul 01 2013 - 22:00:04 PDT
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