Hello –


You should have also specified “glen” or “fglen”/”cglen” in the input file.  Those determine the grid lengths.  The grid center is set by the “gcent” or “fgcent”/”cgcent” keywords.





Nathan Baker

Pacific Northwest National Laboratory




From: nandigana vishal [mailto:nandiganavishal@gmail.com]
Sent: Saturday, May 11, 2013 6:33 PM
To: apbs-users@googlegroups.com
Subject: Re: [apbs-users] query on dielx command


Hi Keith,


Thanks very much Keith. I understood the format of dumping now. 


Also I have the following query. 


In my problem,  I had generated a ssdna of poly(dA)40 and converted it into pqr file. Then, in my apbs.in input file I specify only the grid spacing. However, I would like to know how does APBS decide the domain for the calculations, and choose the origin, etc. 





Vishal Nandigana
PhD Student, Mechanical Engineering
University of Illinois at Urbana Champaign,
Beckman Institute for Advanced Sciences
Room no - 3213,
Illinois 61820,

On Saturday, May 11, 2013 8:18:14 PM UTC-5, Keith Callenberg wrote:

Hi Vishal,


You can find the specification describing the dx file format in the APBS user guide here:





On Sat, May 11, 2013 at 8:58 PM, nandigana vishal <nandiga...@gmail.com> wrote:

Hi Nathan,


I was trying to understand the command dielx and understood it represents the dielectric constant of the material in the x direction. Similarly diely and dielz represent the dielectric constant in the y and z directions. 


Using the write dielx dx eps_x command I had output the dielectric constants in the x direction into the file eps_x. I thought the eps_x file would be a vector, where every value would correspond the diectric constant in that particular x position. However, I noticed that it is a matrix. Please let me know what does the second and third column values represent. 







Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and
their applications. This 200-page book is written by three acclaimed
leaders in the field. The early access version is available now.
Download your free book today! http://p.sf.net/sfu/neotech_d2d_may
apbs-users mailing list


Keith M. Callenberg
Ph.D. Candidate, Computational Biology
Carnegie Mellon University-University of Pittsburgh