AMBER Archive (2006)

Subject: Re: AMBER: 1st 2 lines of restart files

From: Steven Winfield (saw44_at_cam.ac.uk)
Date: Thu May 25 2006 - 06:50:18 CDT

Hi,

This is the current simulation time.
See http://amber.scripps.edu/format.html

Steve.

On Thu, 25 May 2006, hayden wrote:

>
> Dear Amber users
>
> I am currently developing some code for doing various manipulations of
> protein coordinates. This inevitably means I need to create restart files on
> the fly. My current strategy has been to generate coordinates and velocity
> values in an amber format and then append them to a standard file that
> contains 2 lines of a usual restart file. However, I have noticed that the
> first 2 lines of the restart file are not superfluous, and that my choice of
> these first 2 lines affect drastically the nature of my dynamics.
>
> Consider the first few lines of a restart file below:
>
> &SP
>
> 60 0.8001000E+01
> 3.7126232 5.4046935 -0.6650335 3.6504821 4.4052897 -0.5330020
> 4.8881885 6.0726386 -0.0402767 5.2856881 6.8288725 -0.7171849
> 4.2857077 6.7669687 1.2096267 3.3414002 7.2507716 0.9599908
>
> The first line appears to indicate the first residue in the sequence (this
> is fine I take this into account when creating the restart file). The second
> line begins with the no. of atoms being considered (this is no problem
> either). However, the third piece of information is not obvious, and it's
> value appears to affect the energies of the system when I restart sander.
>
> My Question is: What does this "third piece" of information indicate?
>
> Many thanks
>
> Hayden
> ______________________________________________
> Hayden Eastwood
> Perdita Barran Research Group
> Joseph Black Building
> Edinburgh University
> West Mains Road
> EH9 3JJ
>
> Tel: 0131 650 4773
> e-mail: s0237717_at_sms.ed.ac.uk
> Research page:http://homepages.ed.ac.uk/pbarran/PBRG/
> "You have to be an academic to believe some things; no ordinary person would
> be so stupid." -George Orwell
>
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