AMBER Archive (2008)

Subject: Re: AMBER: Query on restart file

From: Neha Gandhi (n.gandhiau_at_gmail.com)
Date: Thu Oct 30 2008 - 21:22:49 CDT

Dear Dr. Duke,

Thank you very much, yes you are correct. But I didnot use iwrap till 17ns,
as you mention there are issues with diffusion etc. As per your
recommendation I ll use iwrap during previous trajectory, it would ok, as
energies wont be affected rather than running all the production runs all
over again with iwrap=1.

Many thanks,
Regards,
Neha

2008/10/31 Robert Duke <rduke_at_email.unc.edu>

> Check the restart for overflow of the file format (search for a short
> string of '****' where you would expect a number. You are probably running
> without iwrap = 1, right? Well, after a while, the primary images will go
> into space with a coordinate greater than the file format can handle (which
> is 9999. to -999. if memory serves - it is the negative overflow that kills
> you). When this happens, you must go back to your last good restrt and run
> at least 1 step with iwrap=1 set in &cntrl. This will wrap the atom primary
> images back into the primary unit cell (coordinate values closest to 0.).
> This is not done routinely because it interferes with things like diffusion
> measurements, but most folks don't want to do that anyway. There is
> probably lots more info on this problem in the reflector archives. Some
> folks just leave iwrap on all the time. I typically just check every 20
> nsec or so and wrap if things are getting close to overflowing (overflowing
> in 17 nsec seems fast, but your system may have some hotter molecules than
> the ones I routinely deal with).
> Regards - Bob Duke
>
> ----- Original Message -----
> *From:* Neha Gandhi <n.gandhiau_at_gmail.com>
> *To:* amber_at_scripps.edu
> *Sent:* Thursday, October 30, 2008 9:49 PM
> *Subject:* AMBER: Query on restart file
>
> Hi Amber community,
>
> I ran 17 ns of production runs (each trajectory file consist of 500 ps with
> 50 frames). I tried to run another 500 ps after 17ns but it just says cannot
> read coordinates from the previous .rst file. When I checked , there is no
> spelling error and I checked the previous rst files. To verify I again run
> the 16th ns md again and no issues with it. Only thing I cannot further run
> MD after 17th ns? What could be the problem and the possible solution? I m
> following the mm-pbsa tutorial in amber.
>
> Many thanks,
>
> --
> Regards,
> Neha Gandhi,
> School of Biomedical Sciences,
> Curtin University of Technology,
> GPO Box U1987 Perth,
> Western Australia 6845
>
> 

-- 
Regards,
Neha Gandhi,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845

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