[gmx-users] Regarding simulation radioactive material

Justin Lemkul jalemkul at vt.edu
Wed May 10 22:05:38 CEST 2017

Please keep the discussion on the gmx-users mailing list.  I am not a private 
help service.

On 5/10/17 2:58 PM, RAHUL SURESH wrote:
> Dear Justin
> I would like to simulate a radioactive peptide.. I think this is the  first of
> its kind.  I wish to study interaction between Radioactive peptide and a protein.
> To make it simple if I want to convert all my carbon into radioactive isotopes
> c14, and simulate is it possible ?

Possible, yes, but not correct.  If you change the mass of any atoms, you change 
their vibrational frequencies, which means you need to reparametrize all the 
bonded terms involving the modified atom types.  That means bonds, angles, and 
dihedrals.  Whether or not this gives anything meaningful in terms of modeling 
the interactions of a radioactive peptide with a larger protein is another 
question.  If you're not changing any elements of the nonbonded terms (which you 
likely shouldn't) then I doubt the interactions will be different in any 
statistically meaningful way from the default parameters.  Re-doing bonded 
parameters is a LOT of work.


> References, I have found few  experimental papers on this. Where they have Used
> isotopes of hydrogen. Tritium instead of hydrogen.
> If any information regarding this is available, will be a great use for me.
> Thank you.
> Sorry for writing in person
> --
> */Regards,/*
> */Rahul Suresh/*
> */Research Scholar/*
> */Bharathiar University/*
> */Coimbatore/*


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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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