Hi,
On Wed, Sep 13, 2017 at 9:49 PM, 杨满意 <ymy0664.163.com> wrote:
> I have test it as follow: (the solvent is MeOH)
> radial RDF 0.02 15 :2-494 :1.N1 density 0.0149
What you describe seems like a normalization issue. The first mask
which selects your MeOH molecules selects all atoms in each methanol
molecule (6). The reference (bulk) density is in molecules/Ang^3, not
atoms, which is probably where that factor of 6 comes in. So either
adjust your reference density to account for this or just selected one
atom from the methanol molecule, e.g. either the C or O atom.
-Dan
> I found the final convergency value is 6 but not 1, why? please tell me how wo solve this problem?
> Thanks!
>
>
> At 2017-09-13 21:39:48, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
>>Hi,
>>
>>On Tue, Sep 12, 2017 at 11:58 PM, 杨满意 <ymy0664.163.com> wrote:
>>> Dears:
>>> I have read the usage of 'radial' in the Amber2016 Manual,but I still have some questions.
>>> radial <outfilename> <spacing> <maximum> <solvent mask1>
>>> [<solute mask2>] [noimage] [density <density> | volume]
>>> [center1 | center2 | nointramol] [<name>]
>>> [intrdf <file>] [rawrdf <file>]
>>> If I want to calculate the N(from solute) ---O1 (from solvent MeOH), the input should write like that, right?
>>> radial RDF-450K-3 0.02 15 :2-494.N1 :1.O1 density 0.0149
>>
>>If what you want is the RDF of all solute 'N1' atoms to a single O1
>>atom in residue 1 then this will probably give you the output you
>>want.
>>
>>-Dan
>>
>>
>>
>>--
>>-------------------------
>>Daniel R. Roe
>>Laboratory of Computational Biology
>>National Institutes of Health, NHLBI
>>5635 Fishers Ln, Rm T900
>>Rockville MD, 20852
>>https://www.lobos.nih.gov/lcb
>>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Sep 18 2017 - 11:30:05 PDT
