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

Dallas Warren dallas.warren at monash.edu
Thu Jun 13 20:47:04 CEST 2019

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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