Dear Dan:
Sorry, I have made a mistake.
I want the RDF of the single 'N1' atoms in residue 1 to all solvent 'O1' atom (residues 2-494),I can write it like this, right?
radial RDF 0.02 15 :2-494.O1 :1.N1 density 0.0149
But now, I still want to know How to calculate the RDF of the single 'N1' atoms in residue 1 to all solvent all atoms (residue 2-494), what should I do?
I have test it as follow: (the solvent is MeOH)
radial RDF 0.02 15 :2-494 :1.N1 density 0.0149
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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Received on Wed Sep 13 2017 - 19:00:03 PDT
