[gmx-users] RDF analysis with respect to center of mass of rotein

Justin Lemkul jalemkul at vt.edu
Fri Sep 19 22:36:07 CEST 2014

On 9/18/14 4:45 PM, Carlos Navarro Retamal wrote:
> Hi Justin,
> First of all thanks for your reply.
> It worked, but i’m getting weird results.
> When i measured the RDF between:
> Protein (COM) - Glycerol (the entire molecule)  i got a huge pick at 0.022 nm, which doesn’t make any sense (because i presumed that at this distance there must be a steric effect) am i right? Because this is my first time considering the center of mass of a molecule, so i don’t really know which distances are ‘normal’ are which are not considering one group as a COM of the protein.
> i used the next command:
>> g_rdf -f npt_production.xtc -com -s npt_production.tpr-o TEST-glycerol.xvg
> group 1: Protein
> group 2: GOL (glycerol molecules)

Indeed a distance of 0.022 nm would be physically impossible (that's 1/5 the 
length of a C-H bond!), so it's something else.  I wouldn't expect it to be an 
issue, but note that g_rdf warns about the value of nrexcl in the topology. 
Probably some intramolecular terms are contributing in a weird way.  If this is 
the only bizarre peak, you can probably safely ignore it using g_rdf -cut 0.05 
or something similar.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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