Re: [Apbs-users] Vpmg_fillco error - help

[Yong H. <yhu...@gm...>]

Hello,

In this case, you just need to increase the coarse grid length (e.g., from
cglen 80 80 80 to cglen 160 160 160) to cover those off-the-mesh atoms, and
the Vpmg_fillco errors should go away. Following are my answers to your
questions:

1. How does one determine the optimal grid dimension? (Or, is it trial
based?)

A: apbs/tools/manip/inputgen.py should be a good source (or reference) for
choosing appropriate parameters for APBS calculation.


2. Is there any aprior way of knowing what are all the grid dimensions that
are compatible with nlev = 4? Currently, I reset it based on the resetting
value the program gives. (I am also yet to understand what nlev = 4 means.)

A. The definition of nlev can be found here:

http://www.poissonboltzmann.org/apbs/user-guide/running-apbs/input-files/elec-input-file-section/elec-keywords/nlev

nlev is now a deprecated keyword in APBS. There is no need to specify nlev
in your APBS input file, APBS will determine the depth of multigrid
hierarchy according to your grid points.


3. What is the unit of the grid dimension - angstrom or nanometers?

A: Angstrom.

Thanks,

Yong


On Sat, Sep 18, 2010 at 9:32 PM, Vigneshwar Ramakrishnan <
vms...@gm...> wrote:

> Dear Dr. Baker,
>
> Thank you very much for your attention. I am herewith attaching the input
> file and the PQR files.
>
> Sincerely,
> Vignesh
>
>
>
> On Sun, Sep 19, 2010 at 10:10 AM, Baker, Nathan <Nat...@pn...>wrote:
>
>>  Hello –
>>
>>
>>
>> Can you please send your APBS input file and PQR file to help us
>> troubleshoot the problem?
>>
>>
>>
>> Thanks,
>>
>>
>>
>> __________________________________________________
>> *Nathan Baker*
>> Chief Scientist for Signature Science
>> Pacific Northwest National Laboratory
>>
>>
>>
>> *From:* Vigneshwar Ramakrishnan [mailto:vms...@gm...]
>> *Sent:* Saturday, September 18, 2010 3:29 AM
>> *To:* apb...@li...
>> *Subject:* [Apbs-users] Vpmg_fillco error - help
>>
>>
>>
>> Dear Users,
>>
>> I am a newbie to APBS and I am yet trying to understand the theory and
>> functioning of the APBS solver. So, pardon me if my questions are naive.
>>
>> I am trying to calculate the binding energy of a protein-DNA complex.
>> During the polar energy calculation, I get the following error:
>>
>> Vpmg_fillco:  Atom #87 at (39.560, 6.880, 66.270) is off the mesh (for
>> cubic splines!!) (ignoring this atom):
>> Vpmg_fillco:    xmin = 2.65, xmax = 82.65
>> Vpmg_fillco:    ymin = 7.4615, ymax = 87.4615
>> Vpmg_fillco:    zmin = 9.235, zmax = 89.235
>>
>> for a number of atoms. Searching through the lists, I found that I need to
>> increase the grid dimensions (the current one I am using is 161 161 161). I
>> increased it up until 225 (compatible with nlev = 4) but still I get the
>> error.
>>
>> My questions are:
>>
>> 1. How does one determine the optimal grid dimension? (Or, is it trial
>> based?)
>> 2. Is there any aprior way of knowing what are all the grid dimensions
>> that are compatible with nlev = 4? Currently, I reset it based on the
>> resetting value the program gives. (I am also yet to understand what nlev =
>> 4 means.)
>> 3. What is the unit of the grid dimension - angstrom or nanometers?
>>
>> Thank you very much,
>> Vignesh
>>
>>
>>
>> --
>> R.Vigneshwar
>> Graduate Student,
>> Dept. of Chemical & Biomolecular Engg,
>> National University of Singapore,
>> Singapore
>>
>> "Strive for Excellence, Never be satisfied with the second Best!!"
>>
>> I arise in the morning torn between a desire to improve the world and a
>> desire to enjoy the world. This makes it hard to plan the day. (E.B. White)
>>
>
>
>
> --
> R.Vigneshwar
> Graduate Student,
> Dept. of Chemical & Biomolecular Engg,
> National University of Singapore,
> Singapore
>
> "Strive for Excellence, Never be satisfied with the second Best!!"
>
> I arise in the morning torn between a desire to improve the world and a
> desire to enjoy the world. This makes it hard to plan the day. (E.B. White)
>