[gmx-users] RDF between larger molecules

[Justin Lemkul]

On 1/20/20 10:00 AM, Gmx QA wrote:
> Thanks Justin!
>
> Can you also comment on the other issue, the lack of smoothness? I guess
> this is because I don't have that many individual coms per bin to
> accurately compute the rdf? At least I think that makes sense since when I
> increase the value of -bin in gmx rdf I get an increase in "smoothness" and
> fewer "jump" back and forth.
>

It's just sampling. RDF analysis was designed for pure liquids, in which 
there are a huge number of the same type of interaction. You have a 
heterogeneous system, so in the absence of much longer simulations, 
you're not going to get smooth RDFs.

-Justin

>
> Den mån 20 jan. 2020 kl 15:50 skrev Justin Lemkul <jalemkul at vt.edu>:
>
>>
>> On 1/20/20 9:48 AM, Gmx QA wrote:
>>> Hi list,
>>>
>>> I am working on a system that contains lipids, but since there is no
>> water
>>> present they do not form a typical bilayer.
>>>
>>> In these systems I also have some smaller drug-like molecules. What would
>>> be the best way to get a proper rdf-function between the lipids and the
>>> drugs? Since both types of molecules are larger than single atoms, I
>> tried
>>> to calculate a com-com rdf using
>>>
>>> -selrpos whole_mol_com -seltype whole_mol_com
>>>
>>> but the resulting curve is very rugged (i.e. not as smooth as
>>> the atom-rdf's typically shown). The minimum distance (the distance
>>> below which the pdf is zero) also appears to be quite small, since one
>> the
>>> molecules is a lipid I would have expected a larger distance than
>>> the corresponding value seen in e.g. an oxygen-oxygen rdf for water.
>>>
>>> Might all of this be consequences of the fact that I have a com-com rdf
>>> between a limited number of molecules?
>> Yes, likely. You could in principle have a COM-COM RDF value very close
>> to r=0 if a lipid were to wrap around a drug molecule, so I don't think
>> any of your results are unexpected.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================