> One minor point - to get the correct normalization, typically what you
> want is to have the first mask be the one with many atoms (in this
> case the water), and the second to have fewer atoms (solute).
Yes, sorry. I was not very clear on this though the “solvent”/“solute” situation is covered in the documentation.
// Gustaf
> On 5 Jun 2018, at 15:05, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> It's the combined (think of it as averaged) RDF of each atom in the
> mask. If you want the geometric center of the mask you have to use the
> center1 or center2 keyword(s) (for center mask 1 and mask 2
> respectively).
>
> One minor point - to get the correct normalization, typically what you
> want is to have the first mask be the one with many atoms (in this
> case the water), and the second to have fewer atoms (solute).
>
> Hope this helps,
>
> -Dan
>
> On Tue, Jun 5, 2018 at 8:53 AM, <diego.soler.uam.es> wrote:
>> Thank you so much! That worked for me. One more quick question. If
>> in the first mask (:XXX.YYY, in Olsson's message) I put two or more
>> atoms, the output is just a single RDF. What is reference/origin of
>> that RDF? Is it the Center of Mass of those atoms, or what?
>>
>> Best,
>>
>> Diego SP
>>
>>
>>
>> Quoting Gustaf Olsson <gustaf.olsson.lnu.se>:
>>
>>> Something like this should do it…
>>>
>>> parm ../[YOUR-PRMTOP]
>>> trajin ../[YOUR-TRAJECTORY/(IES)]
>>> radial [OUTPUT] 0.1 20 :XXX.YYY :ZZZ intrdf [OUTPUT] volume nointramol
>>>
>>> Where XXX is the residue, YYY is the atom and ZZZ is “WAT”/“HOH" or
>>> whatever water residues are called in your simulation.
>>>
>>> The “intrdf” includes the integrated RDF function values in a
>>> separate column in the [OUTPUT] file though can be skipped if not of
>>> interest to you.
>>>
>>> Just check the documentation for details.
>>>
>>> // Gustaf
>>>
>>>> On 4 Jun 2018, at 17:08, diego.soler.uam.es wrote:
>>>>
>>>>
>>>> Hi,
>>>>
>>>> After having run a simulation, I would like, given a certain atom A,
>>>> to calculate the radial distribution function of waters with respect
>>>> to atom A. That is, I would like to use the info from the simulation
>>>> to construct a function P(r) giving me the average number of water
>>>> molecules at a distance r of atom A.
>>>>
>>>> In principle this should be doable by hacking the appropriate data out
>>>> of the output file (the one with the coordinates), but I have no idea
>>>> of how to achieve this.
>>>>
>>>> I don't know if it is possible to do this easily in AMBER.
>>>>
>>>> Thank you for your time!
>>>>
>>>>
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>>>
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>>
>>
>>
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Received on Tue Jun 05 2018 - 06:30:04 PDT
