Re: [AMBER] iwrap=1 "can mess up diffusion and other calculations"

From: Robert Molt <>
Date: Tue, 24 Nov 2015 22:02:49 -0500

thank you

On 11/24/15 9:57 PM, Jason Swails wrote:
> On Tue, Nov 24, 2015 at 8:45 PM, Robert Molt <> wrote:
>> The manual states that iwrap=1 "...can mess up...and other
>> calculations." Can it be specified what these other calculations are?
> ​Diffusion and diffusion-related calculations. Anything that depends on
> tracking a *particular* particle's trajectory​ through time will be messed
> up by imaging/iwrap=1 (since the coordinates specified for a particular
> atom may change from one image to another during the course of the
> simulation).
> However, assuming you have a continuous time series of trajectory files,
> the "unwrap" command in cpptraj will reverse the effects of "iwrap=1" and
> allow you to perform these kinds of calculations.
> All the best,
> Jason

Dr. Robert Molt Jr.
AMBER mailing list
Received on Tue Nov 24 2015 - 19:30:03 PST
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