Hi,
On Sat, Nov 6, 2021 at 12:19 PM Michael Shokhen
<michael.shokhen.biu.ac.il> wrote:
> I have identified that the error source is the command “autoimage origin”
This isn't an error. You've simply imaged the system in a different
way. With periodic boundary conditions, both pictures are equivalent.
The 'autoimage' command by default will try to center the picture on
the first molecule. Based on the results from 'autoimage', it seems
like you may need more of a buffer in your system (unless for some
reason you need that particular concentration).
-Dan
> in the cpptr_pdb.in file:
> parm ../mc.prmtop
> trajin mdcrd 700000 700000
> autoimage origin
> cpptraj_pdb.in
> trajout heat.pdb pdb
> run
> quit
> The autoimage origin command must be deleted there.
> See the attached figure for illustration.
> Michael
> email: shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
>
> [cid:731c1029-085d-47c0-88a0-9d44a1e56365]
> ________________________________
> From: David A Case <david.case.rutgers.edu>
> Sent: Friday, November 5, 2021 3:30 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] water box corrupted by minimization
>
> On Thu, Nov 04, 2021, Michael Shokhen wrote:
> >
> >The periodic water box is corrupted by minimization procedure.
> >See scripts and figures below.
> >I need your advice how to resolve the problem.
>
> Here is a similar report:
>
> https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Farchive.ambermd.org%2F202110%2F0048.html&data=04%7C01%7Cmichael.shokhen%40biu.ac.il%7Ce2c416cdf5b64bec2d5108d9a06081b6%7C61234e145b874b67ac198feaa8ba8f12%7C1%7C0%7C637717159049907820%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=PhqZffoD83nWbPe1yNrpYfGc%2FFUIJTP48ecTeSyVxjM%3D&reserved=0
>
> Tom lists some ideas for exploring what is going on, and suspects that it is
> "just" a visualization artifact. It's not clear that the original poster
> last month ever supplied any files that would allow one to reproduce the
> problem, so if you could do that, it would probably help.
>
> ....dac
>
>
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Received on Wed Dec 01 2021 - 08:30:03 PST
