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

[Justin Lemkul]

On 9/19/14 4:54 PM, Carlos Navarro Retamal wrote:
> I Justin,
> Thanks for your reply.
> Sadly, that’s not the only bizarre peak,as you can see on the next image:
> http://cl.ly/1B3B2y3I0o1R
> This is how it looks when i don’t consideren the COM as a reference:
> http://cl.ly/3m0d2W2y0N1Y
> What; i your opinion,  could be the problem?

No idea, aside from the nrexcl issue I mentioned before.  I don't know exactly 
why that would be a problem, but that's all I could suggest.  Has the trajectory 
been manipulated in any way, e.g. with trjconv?

-Justin

> I think i’ll just have to use the second image to show the RDF.
> Thanks a lot for your valuable help,
> Best Regards,
> Carlos
>
>
> --
> Carlos Navarro Retamal
> Bioinformatic engineer
> Ph.D(c) in Applied Science, Universidad de Talca, Chile
> Center of Bioinformatics and Molecular Simulations (CBSM)
> Universidad de Talca
> 2 Norte 685, Casilla 721, Talca - Chile
> Teléfono: 56-71-201 798,
> Fax: 56-71-201 561
> Email: carlos.navarro87 at gmail.com or cnavarro at utalca.cl
>
>
> On Friday, September 19, 2014 at 5:35 PM, Justin Lemkul wrote:
>
>>
>>
>> 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
>>
>> --
>> ==================================================
>>
>> 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 (mailto:jalemkul at outerbanks.umaryland.edu) | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
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-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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