Re: [Apbs-users] Grid spacing and down sampling

[Nathan B. <ba...@cc...>]

Hello --

> 1. Let's say that I want to solve the potential with a uniform grid  
> spacing of 0.5 Angstroms in each direction. I'm using mg-para with  
> async, and am attempting to modify the .in file generated by  
> inputgen.py. It seems that it automatically sets 'dime' and then  
> 'cglen' and 'fglen' to enclose the region of the protein of  
> interest, ensure proper overlap, etc. Is there a simple way to  
> force the potential to have the desired grid spacing after mergedx  
> combines all of the .dx potential files?

I'm going to Cc Dave Gohara to help with the details on using mergedx  
to do this...

> 2. Are there any tools already in place that would down sample the  
> merged potential energy file to a coarser grid spacing (e.g. going  
> from a 0.5 x 0.5 x 0.5 Angstrom grid spacing to a 2.0 x 2.0 x 2.0  
> Angstrom grid spacing)?

...however, you can also modify the value.c (multivalue.c) or use the  
Python wrapper vgrid.py to do very similar tasks.  You might look  
over those fils and see if they make sense.  Please let us know if  
you need any help.

Thanks,

Nathan

> Thanks in advance for any assistance you are able to provide.
>
> Josh
>
>
> ---------------------------------------------------------------------- 
> --------------------------------
> Joshua L. Adelman
> Biophysics Graduate Group              Lab: 510.643.2159
> 218 Wellman Hall                                Fax: 510.642.7428
> University of California, Berkeley     http://nature.berkeley.edu/ 
> ~jadelman
> Berkeley, CA 94720 USA                   jad...@be...
> ---------------------------------------------------------------------- 
> --------------------------------
>
>
>
>
> ---------------------------------------------------------------------- 
> ---
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to  
> share your
> opinions on IT & business topics through brief surveys - and earn cash
> http://www.techsay.com/default.php? 
> page=join.php&p=sourceforge&CID=DEVDEV________________________________ 
> _______________
> apbs-users mailing list
> apb...@li...
> https://lists.sourceforge.net/lists/listinfo/apbs-users

--
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/