Sorry but I don’t know of a good way to visualize the best.  I’ve done it in the past with VMD using a very complicated Tcl script – however, there must be an easier way.  Tools like OpenDX used to support this type of visualization.

 

--

Nathan Baker

Pacific Northwest National Laboratory

+1-509-375-3997

http://nabaker.me

 

From: nandigana vishal [mailto:nandiganavishal@gmail.com]
Sent: Saturday, May 11, 2013 7:59 PM
To: apbs-users@googlegroups.com
Cc: nandigana vishal; APBS-USERS mailing list (apbs-users@lists.sourceforge.net); Baker, Nathan
Subject: Re: [apbs-users] query on dielx command

 

Thanks Nathan. 

 

I indeed have the following lines, and understood what each command is trying to do. 

 

    dime 97 97 321                               # number of grid points per processor 

    fglen 41.2556 49.0120 158.7180    # Specifies the fine mesh domain lengths in a multigrid focusing calculation 

    fgcent mol 1                                    # center of the fine grid, chosen on the molecule's center

    cglen 41.2556 49.3204 235.8206      #Specify the length of the coarse grid (in a focusing calculation) for an automatic multigrid. This is the starting mesh, so it should be large enough to complete enclose the biomolecule and ensure that the chosen boundary condition

 

Now is it possible to visualize the generated output say potential along with the mesh using any of your tools to get a better understanding of the mesh. 

 

Thanks

 

Regards

Vishal

 


On Saturday, May 11, 2013 9:05:19 PM UTC-5, Baker, Nathan wrote:

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.

 

Thanks,

 

--

Nathan Baker

Pacific Northwest National Laboratory

+1-509-375-3997

http://nabaker.me

 

From: nandigana vishal [mailto:nandiga...@gmail.com]
Sent: Saturday, May 11, 2013 6:33 PM
To: apbs-...@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. 

 

Thanks

 

Regards,

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


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:

 

Keith

 

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. 

 

 

Thanks

 

Regards,

Vishal


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--
Keith M. Callenberg
Ph.D. Candidate, Computational Biology
Carnegie Mellon University-University of Pittsburgh
kmc...@{pitt,cmu}.edu
http://www.pitt.edu/~kmc112/