Re: [AMBER] How to save reimaged trajectory file during MD?

From: Daniel Roe <>
Date: Mon, 2 Oct 2017 09:05:16 -0400

On Wed, Sep 27, 2017 at 2:35 PM, Ravi Abrol <> wrote:
> Thanks.
> So, for complex cases is it better to not use iwrap option but use cpptraj
> to reimage?
> I mean, would that make cpptraj's job easier?

Yes, although in my experience 'autoimage' in more recent versions of
cpptraj does a good job of re-imaging, especially if you properly
specify the anchor/use the 'moveanchor' option as appropriate for more
condensed systems.

If you want to run with iwrap=0 just make certain that you are using
NetCDF trajectories (ioutfm=1) and restarts (ntxo=2). Note that those
have become the default formats in Amber versions 16 and up.


> Ravi
> On Tue, Sep 26, 2017 at 10:17 AM, David A Case <>
> wrote:
>> On Tue, Sep 26, 2017, Ravi Abrol wrote:
>> >
>> > I want to save the .nc files during MD in such a way that I don't need to
>> > use cpptraj later to reimage/center etc.
>> > The .rst files are written during MD and they don't need to be reimaged
>> in
>> > my experience, so can't the .nc
>> > be written that way during MD?
>> Be wary of the second statement: the iwrap=1 option in sander/pmemd is fine
>> for very simple systems, but has nowhere near the flexibility that cpptraj
>> has
>> for complex examples. (I've long been in favor of removing the iwrap
>> option
>> from the MD codes, but there seem to be just enough cases where it is
>> useful to
>> prevent this notion from gaining traction.)
>> I think the answer to your basic question is that developers haven't felt
>> the
>> need to have this option for their own work, and haven't seen pressure from
>> users to implement it.
>> ....dac
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>> AMBER mailing list
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Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Mon Oct 02 2017 - 06:30:03 PDT
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