AW: The size of a periodic cell in NAMD operation

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Sep 03 2012 - 01:45:48 CDT

Hi,

I'm not sure, but if you doesn't know how big the system is, that he has
build on his own (or try to build), is it good to measure the box size from
that system, if we don't know if it already exist. Lastly he should know the
box size at the point where he solvated the system.

It would be also interesting which forcefield you are using, or what tools
to build the box.

So, if you have already solvated the system, you should know what box you
used for that. If you are going to build a system and do not know how to set
the box, this is a different thing. Usually, if there is nothing to be
continued periodically, like a surface, you can just use the bounding box of
the solute, and increase it by an amount of safety distance to each
dimension, depending on how big the system already is and if you want
periodic interactions of the solute. If you don't want to interact the
protein with its periodic copies for example, set in more large.

If this doesn't help, please provide more detailed information at which step
of building up a simulation you are stucked.

Good luck.

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Chris Harrison
> Gesendet: Samstag, 1. September 2012 02:56
> An: Patrick Chiu
> Cc: namd-l_at_ks.uiuc.edu
> Betreff: Re: namd-l: The size of a periodic cell in NAMD operation
>
> Patrick Chiu <patrick817us_at_yahoo.com> writes:
> > Date: Fri, 31 Aug 2012 16:45:19 -0700 (PDT)
> > From: Patrick Chiu <patrick817us_at_yahoo.com>
> > To: namd-l_at_ks.uiuc.edu
> > Subject: namd-l: The size of a periodic cell in NAMD operation
> > X-Mailer: YahooMailClassic/15.0.8 YahooMailWebService/0.8.121.416
> >
> > How do I decide the size of a periodic cell in NAMD operation. Is it
> just big enough to hold the model containing protein and waters?
> > Yours sincerely
> > NAMD user
> > See Hong Chiu
> >
>
> Typically, yes.
>
> If you put the below proc in a file (get_cell.tcl) and load it into the
> TkConsole (see Extensions > TkConsole) in VMD with "source
> get_cell.tcl", then
> load your system and finally type in the TkConsole get_cell, it will
> output the
> necessary vectors and center.
>
> proc get_cell {{molid top}} {
> set all [atomselect \$molid all]
> set minmax [measure minmax \$all]
> set vec [vecsub [lindex \$minmax 1] [lindex \$minmax 0]]
> puts "cellBasisVector1 [lindex \$vec 0] 0 0"
> puts "cellBasisVector2 0 [lindex \$vec 1] 0"
> puts "cellBasisVector3 0 0 [lindex \$vec 2]"
> set center [measure center \$all]
> puts "cellOrigin \$center"
> \$all delete
> }
>
>
> Best,
> Chris
>
>
> --
> Chris Harrison, Ph.D.
> NIH Center for Macromolecular Modeling and Bioinformatics
> Theoretical and Computational Biophysics Group
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>
> http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078
> http://www.ks.uiuc.edu/~char Fax: 217-244-6078

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