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#37585 - 07/26/19 05:15 PM Rdfsol command ussage
aad Offline
Forum Member

Registered: 07/18/19
Posts: 6
Loc: NY
Hello,
I am fairly new to this so apologies it this is a silly question.
I am trying to use the rdfsol command in charmm to calculate the radial distribution function of hydroxide ion in a system of water molecules. The command line is as follows:

rdfsol rdf 10 seta water setb sele atom main 1 O1 end firstunit 51 nunit 1
!rdfsol rdf 11 seta water setb water firstunit 51 nunit 1

here I have tried to specify set A as water molecules and set B as the Oxygen atom of the hydroxide ion

I am having trouble with deciphering the output file. I have 4 different columns where the first column is clearly the distance. The next 2 columns has various fluctuating values with no specific trend while the last column is all 0s. Is there a specific code that I can use that will make the output file easier to understand?

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#37586 - 07/29/19 05:08 AM Re: Rdfsol command ussage [Re: aad]
lennart Online   content

Forum Member

Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
I'm not familiar with rdfsol, but you can use the COOR ANALysis command instead (see corman.doc (or corman.info)). It gives three columns of output data:
r,g(r), integral of g(r)
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#37588 - 08/01/19 12:53 PM Re: Rdfsol command ussage [Re: aad]
aad Offline
Forum Member

Registered: 07/18/19
Posts: 6
Loc: NY
Thank you for your input Dr. Nilsson

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