AMBER Archive (2004)

Subject: Re: AMBER: image and restart problems

From: Andy Purkiss (a.purkiss_at_mail.cryst.bbk.ac.uk)
Date: Tue Jun 29 2004 - 08:05:48 CDT

Dear Steve,

I think that you are suffering from the protein picking up translational
motion. You have NSCM = 0, so this motion is not removed from the
system. Try setting nscm = 1000, to remove the translational momentum. I
have seen similar problems when setting nscm = 0.

Andy Purkiss

On Tue, 2004-06-29 at 13:56, Steve Seibold wrote:
> Hello
>
> I am running a long (5-20 ns) MD simulation with a homodimer with
> explicit waters. After about 4 ns I noticed that my restart files were
> corrupted. The coordinates in them were replaced with "********" in
> many places: as shown below:
>
> 18273 0.1137100E+05
>
> -458.5618828************ 865.8784605-458.1478773************
> 865.9780753- 459.5624384************
> 865.9971669-458.3306444************ 864.5385748-
> 459.1445772************ 863.8556527-457.4029599************
> 864.3070980
>
> Thinking that the problem might be that this was an image problem with
> the water molecules, I started using "iwrap=1" to wrap the waters back
> into the box. However, after running for 500 ps or so now my homodimer
> has separated from each other AND translated out of the water box.
>
> Can some one please give me some help?
>
> I am attaching my input file.
>
> Thanks, Steve
>
> 

-- 
Cat, n.: Lapwarmer with built-in buzzer.
+---------------------------------------------------------------------+
|  Andy Purkiss, School of Crystallography, Birkbeck College, London  |
|           E-mail   a.purkiss_at_mail.cryst.bbk.ac.uk                   |
|      Phone 020 7631 6869 (Work) or 0776 490 360 (Mobile)            |
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