Thanks very much !!!
At 2017-09-19 02:22:15, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
>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 25 2017 - 05:00:02 PDT
