The thing is that 113 does fit in the nx=3D...= formula with c=3D7 and l=3D3 and that is why it confuses me that APBS choo= ses to re-dime my calculation automatically. Any ideas here?
Are = there max "c" or "l" values that I should stay within to avoid this problem= ?

NOsh:  Bad dime[0]  =3D 113 (3 nl= ev)!
NOsh:  Reset dime[0] to 97 and (nlev =3D 4).

Best regards,
Jesper

On Monday, April 1, 2013 12:07:05 PM UTC-7, patrizio ansalone wrote:<= blockquote class=3D"gmail_quote" style=3D"margin: 0;margin-left: 0.8ex;bord= er-left: 1px #ccc solid;padding-left: 1ex;">

<= br>
On Mon, Apr 1, 2013 at 6:45 PM, Jesper Soeren= sen wrote:
Hi = Patrizio,

Thanks for = the response. It doesn't really help with my current problem, because I can= 't set the nlev=3D5 in an mg-manual calculation, as this is a deprecated ke= yword.

Probably Nathan can answer better then = me to this question. I think that you do not need to set the nlev. In the previous example you fix the num= ber of points in the grid box with the "dime nx ny nz" and the spacing= "grid hx hy hz" then apb= s internally compute the nlev value.&n= bsp;

Secondly, I am using the grid keyword as described, yet I still need to con= trol the size of the grid not just the spacing.
&nbs= p;
you can substitute the keyword grid with glen

example:
glen 50 50 50=

I need a solution for= an Mg-manual calculation to control both of these parameters.
In terms of the nx=3Dc*2^(l+= 1)+1, what value do you use for the "c" constant?

I think that you have two choices:<= /div>
1. fix the grid spacing grid hx hy hz and fix a number of= points dime nx ny nz such that nx*hx ny*hy nz*hz are suffic= iently large to bound the whole protein.
2. fix the "glen Lx Ly Lz" (bounding box sufficiently large tu cover th= e whole protein) and than fix a number of points "dime nx ny" nz.=
In both cases l and c integers  should be comput= ed internally  in apbs.

Patrizio

=
P.S.
These are a subset of possible va= lues of dime taking into account the constraint nx=3Dc*2^(l+1)+1
nx(c,l)=3D

5   &nbs= p;  9    17    33    65
=     9    17    33    65   129=
13    25    49    97=   193
17    33    65 &nbs= p; 129   257
21    41    8= 1   161   321

Best regard= s,
Jesper
<= div>

On Monday, April 1, 2013 9:22:34 AM UTC-7, patrizio ansalone w= rote:
If you use mg-auto you ca= n use dime nx ny nz  with nx=3Dc*2^(l+1)+1 (also for ny and nz) then i= n your case dime 129 129 129 should work with l=3D5. In this case you could= not fix exactly the grid spacing but it depends on  cglen and  fglen. If you use mg-manually = you have to use the following keyword grid  (http://www.poissonboltzmann.<= u>org/apbs/user-guide/running-apbs/input-files/elec-in= put-file-section/elec-keywords/grid)  and fix t= he grid spacings in the = x-, y-, and z-directions:

read =                      = ;                     &nb= sp;
mol pqr born-ion.pqr
en= d

# COMPUTE POTENTIAL FOR SOLVATED STATE
elec name solvated-coarse
mg-manual   &nb= sp;
dime 65 65 65
gr= id 1.0 1.0 1.0
gcent mol 1
= mol 1
lpbe
bcfl sdh
pdie 1.0
sdie 78.54
chgm spl2
&= nbsp;   srfm mol
&nb= sp; swin 0.3
sdens 10.0
tem= p 298.15
calcenergy total
c= alcforce no
write pot dx born-pot-coarse-sol
end

elec name solvated-fine
mg-manual &= nbsp;
dime 65 65 65
=   grid 0.5 0.5 0.5
gcent mol 1
mol 1
lpbe
&nbs= p; bcfl focus
pdie 1.0
sdie= 78.54
chgm spl2
srfm mol
swin 0.3
=     sdens 10.0
temp 298.15
calcenergy total
calcforce no
end

# = COMPUTE POTENTIAL FOR REFERENCE STATE
elec name reference-coarse<= /div>
mg-manual
dime 65 65 65
grid 1.0 1.0 1.0 &= nbsp;
gcent mol 1
mo= l 1
lpbe
bcfl sdh
pdie 1.0
sdie 1.0
&= nbsp; chgm spl2
srfm mol
&nbs= p;   swin 0.3
sdens 10.0
&nbs= p; temp 298.15
calcenergy total
&n= bsp; calcforce no
write pot dx born-pot-coarse-ref<= /div>
end

elec name reference-fine
=   mg-manual
dime 65 65 65
&n= bsp; grid 0.5 0.5 0.5
gcent mol 1
mol 1
&n= bsp; lpbe
bcfl focus
pdie 1.0
sdie 1.0
&nbs= p;   chgm spl2
srfm mol
swin 0.3
sdens 1= 0.0
temp 298.15
calcenergy = total
calcforce no
end

# CO= MBINE TO GIVE SOLVATION ENERGY
print elecEnergy solvated-fine - r= eference-fine end
print elecEnergy solvated-fine end
pr= int elecEnergy reference-fine end

quit

Hope this= helps
Patrizio

On Sun= , Mar 31, 2013 at 5:49 AM, Jesper Soerensen wrote:
Hello,

I'm trying some mg-manual calculations where I am varying the grid resoluti= on by the keyword "grid".
E.g.
grid 1.0 1.0 1.0 or  grid 0.5 0.5 0.5 or ...

At the same time = I want to force the grid to be a certain size, effectively enforcing the "b= uffer"size around the solute.
I thought I could do this by using the "dime" keyword, but APBS keeps = forcing a re-dime:

NOsh:  Bad dime[0] &n= bsp;=3D 113 (3 nlev)!
NOsh:  Reset dime[0] to 97 and (nlev = =3D 4).

Is there a way to work around this? I also tried = to change the nlev keyword, but this is now a deprecated keyword.

Any suggestions?

Best,
Jesper

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------------------------------------------------------------= ---------------

-- ----------------------------------------------------------------= -----------
Patrizio= Ansalone
Postdoc in "Compu= tational Biology"
Dip. Elettroma= gnetismo
I.N.RI.M. - Istituto= Nazionale di Ricerca Metrologica
S= trada delle Cacce, 91 - 10135
Torino, ITALY
e-mail: p.ans...@inrim.it
-----------------------------------------------------------------= ----------
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