Re: [AMBER] NVE Energy/Temperature Drift Issue

From: Daniel Roe <>
Date: Mon, 1 Jul 2013 22:17:59 -0600


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 - 21:30:03 PDT
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