[gmx-users] Details of g_rdf functions in version 4.6.5.

Sun Jun 16 17:37:25 CEST 2019

On 6/16/19 4:21 AM, Henry Vider wrote:
> Thank you, Justin.
>
> However, I meant what is the formula for selecting the atoms for default command line (without specifying -rdf). If I run g_rdf I have several groups available for choosing to calculate the RDF of, and when choosing group Ethyl Acetate to Ethanol I get, as Warren pointed out, RDF for atoms. But what atoms exactly?

The ones you choose. For every atom in the first selection, g_rdf 
computes the distance to all the atoms in the second selection. Again, 
this is described in the manual, along with the mathematics associated 
with it.

-Justin

> Faithfully,
> Henry
>
> From: Justin Lemkul
> Sent: Sunday 16 June, 02:41
> Subject: Re: [gmx-users] Details of g_rdf functions in version 4.6.5.
> To: gmx-users at gromacs.org
>
>
>
>
> On 6/14/19 1:15 AM, Henry Vider wrote:
>> Dear Warren,
>>
>> So if I understand you correctly, does this mean that the g_rdf default settings function starts off with taking my Ethyl Acetate's first atom assigned in *.tpr, then selects Ethanol's first atom and calculates the RDF for this interaction. Now followed by Ethanol's second atom, repeating it until the last Ethanol atom. Then selecting second atom of Ethyl Acetate and goes through the process again. And in the end the RDF is averaged over all these calculated interactions?
>>
>> Or is the formula of calculation some other ?
> The formula for computing an RDF is given in the manual. It's not an
> average, it's a probability function, normalized to bulk density.
>
> -Justin
>
>> Thank you
>>
>> Faithfully,
>> Henry
>>
>> -----Original Message-----
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Dallas Warren
>> Sent: Thursday, June 13, 2019 21:47
>> To: GROMACS users <gmx-users at gromacs.org>
>> Subject: Re: [gmx-users] Details of g_rdf functions in version 4.6.5.
>>
>> The selection you made means you calculated the RDF of all ethyl acetate atoms to all ethanol atoms. The atoms it uses are those in each of the index groups you selected.
>>
>>    The 0.2nm start of the function is reasonable as that is how close the center of two atoms can get.
>>
>> What you want to use is - rdf mol_com and supply a .tpr using - s so it can work out what a molecule is. This will give you 5he COM rdf between the two types of molecules.
>>
>> On Thu, 13 Jun. 2019, 6:41 pm Henry Vider, <henry.vider at ut.ee> wrote:
>>
>>> From: Henry Vider
>>> Sent: Thursday, June 13, 2019 11:37
>>> To: gromacs.org_gmx-users at maillist.sys.kth.se
>>> Subject: Details of g_rdf functions in version 4.6.5.
>>>
>>> Dear GROMACS mailing list,
>>>
>>> I am writing here due to the inconsistencies in my Radial Distribution
>>> Functions (RDF) calculations. Currently I am using v. 4.6.5. of GROMACS.
>>>
>>> I am simulating water-organic binary solvents with a few solute
>>> molecules added into the system. I have simulated a lot of different
>>> compositions for water and organic solvent, but I have kept solute
>>> molecule number constant at 10 molecules. For example, one of the
>>> systems is 10 Ethyl Acetate, 1250 Ethanol and 1240 Water, totaling
>>> 2500 molecules. (As a side question, is this system size appropriate
>>> for studying solute-solvent interactions when I have 10 solute
>>> molecules or should I lower the number of solute
>>> molecules?)
>>>
>>> When initiating g_rdf function with default settings, i.e. only
>>> specifying -f *.xtc , -s *.tpr and -o *.xvg and -cn, I am prompted
>>> with a selection for two groups. In the case of example system, I
>>> choose firstly the Ethyl Acetate group and then Ethanol group which
>>> means I should get RDF of Ethanol molecules distributed around Ethyl
>>> Acetate molecules. However, when looking at the graphical
>>> representation of the RDF, I notice that the function starts at 0.2 nm
>>> which is unreasonably close for molecule. I have come to a conclusion
>>> with the help of GROMACS manual and looking at the short description
>>> of parameters for the g_rdf function displayed when initiating in
>>> linux terminal, that if I do not specify -rdf with something, for example mol_com etc, the RDF-s are calculated with atoms.
>>>
>>> My question is, what atoms is the script choosing automatically if I
>>> do not specify -rdf value? I tried looking at gmx rdf script, but I
>>> could not understand.
>>>
>>> Secondly, in order to get RDF-s calculated for COM Ethyl Acetate and
>>> COM Ethanol, what should be the command line for g_rdf function? I
>>> have tried several things but I am getting different results,
>>> sometimes even RDF-s are abnormal but CN functions seem appropriate.
>>>
>>> Thank you in advance!
>>>
>>> Faithfully yours,
>>> Henry
>>>
>>>
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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
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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

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