[gmx-users] Regarding simulation radioactive material
chris.neale at alum.utoronto.ca
Thu May 11 02:16:20 CEST 2017
Unless you're using a bizarre Hamiltonian that includes mass then you should be able to change masses without affecting equilibrium thermodynamic properties at all, right? Dynamics will of course be altered. Justin's right though, any thermodynamic differences in C14 vs C12 would have to be through reparameterization and you likely couldn't trust any changes in dynamics resulting from first changing the mass.
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: 10 May 2017 16:05:28
To: RAHUL SURESH; Discussion list for GROMACS users
Subject: Re: [gmx-users] Regarding simulation radioactive material
Please keep the discussion on the gmx-users mailing list. I am not a private
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
> */Rahul Suresh/*
> */Research Scholar/*
> */Bharathiar University/*
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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