Dear Thomas Cheatham,
I disabled imaging for only one residue and now the rdf initial plateau
looks fine: it dropped from ~0.8 to zero (and the geometry of the curve
is exactly the same as before, which is encouraging).
By the way you wrote that in this case the problem would be the box size.
My system is a dimer of an 11 residues long peptide and I solvated it with
the following command:
solvateoct dimer TIP3PBOX 11.0
using a radial cut off equal to 10.0 Angs in the simulations.
I used a truncated octahedron to avoid interactions due to rotations of
the dimer and used a distance of 11 Angs (1 Ang greater than the cut off)
for the solvation command.
Therefore I had assumed that the size of the box should be OK.
I hope I am not missing anything fundamental here.
Many thanks in advance.
Best,
Il 16 settembre 2011 14:13, Thomas Cheatham <tec3.utah.edu> ha scritto:
>
> [note: multiple copies of the same message to the reflector are
> discouraged]
>
>> I calculated the radial distribution functions, g(r), of the solvent
>> (water TIP3P) with respect to
>> every atom of each residue of my peptide (from 0.0 Angs up to 6.0
>> Angs), with the following
>> command:
>>
>> radial "name" 0.1 6.00 :WAT :"res"
> ...
>> What I can not understand is why for few residues the value of the
>> g(r) initial plateau is
>> not zero but higher (for instance ~0.13 or ~0.2).
>> I would expect that every initial plateaus is at zero, as atoms have
>> finite dimensions.
>
> The radial command uses the standard ptraj routines to calculate distance
> and they should be working OK, and by default, with periodicity (to find
> the minimum imaged distance).
>
> On output, radial dumps a summary...
>
> PTRAJ RADIAL: dumping radial distribution functions
> 50 visits, 446501 measurements from r = 1.637 to 12.000; max r = 12.000
> Density is 0.03346 (based on volume is 0.09358). Cell volume is 391726.66289
>
> Are "r" values showing up at short distances like 0.13 or 0.2 A?
>
> I would try seeing if there are differences if you disable imaging (add
> "noimage") which would suggest a problem with box size.
>
> An alternative is to use the checkoverlap command to search for short
> contacts (shown below for looking at water around residues 1-100)....
>
> checkoverlap :WAT min 0.0 around :1-100
>
> This will show where the short distances are. --tec3
>
>
>
>
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--
Dr Massimiliano Porrini
Institute for Condensed Matter and Complex Systems
School of Physics & Astronomy
The University of Edinburgh
James Clerk Maxwell Building
The King's Buildings
Mayfield Road
Edinburgh EH9 3JZ
Tel +44-(0)131-650-5229
E-mails : M.Porrini.ed.ac.uk
mozz76.gmail.com
maxp.iesl.forth.gr
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Received on Sun Sep 18 2011 - 10:30:02 PDT
