[gmx-users] Deuterate organic solvent
jalemkul at vt.edu
Sun Sep 29 20:40:23 CEST 2013
On 9/29/13 1:24 AM, Jonathan Saboury wrote:
> I want to run a simulation of cyclohexane in deuterated chloroform.
> I was able to run a sim of cyclohexane in regular chloroform, but unable to
> find how to make a solvent deuterated. I know that pdb2gmx has a -heavyh
> and -deuterate option, would I do it this way? It isn't a protein and would
> assume I would get an error.
pdb2gmx can handle anything for which you provide an .rtp entry; it need not be
There really isn't any need to run pdb2gmx at all; you already have topologies
listed below. If you're trying to deuterate CHCl3, you only need to modify a
couple lines in its .itp file.
> I know these sims are based off of newton's laws of motion, and that is
> pretty much where my understanding stops. I assume that the hydrogen’s have
> a mass of ~1, and that I need to change them to ~2.
> I look at the .itp's generated by acpype and all the masses are set to 0
> (is this alright?) Note: all [atomtypes] are in cyclohexane_GMX.itp.
Masses in [atomtypes] are overridden by values in [atoms], so you do not have
any zero-mass atoms.
> Another problem I see happening that the atomtypes are all sharing the same
> atomtype, so possibly any sp3 C-H bond is going to be deuterated since they
> all share the same definition.
I'm not sure what the issue here is - you want deuterated CHCl3, right? You
will have to change bonded parameters involving the C-D bond (because they won't
be the same as a C-H bond), but any changes made to the CHCl3 topology will not
affect the cyclohexane or any other molecule in the system.
> commands: http://pastebin.com/raw.php?i=jGZV8k2t
> cyclohexane_GMX.itp: http://pastebin.com/raw.php?i=Q6MrURmN
> chloroform_GMX.itp: http://pastebin.com/raw.php?i=pAHaUSVv
> Entire folder download: http://www.sendspace.com/file/frc1uy
> Is there an automatic way to have a specific solvent be deuterated?
> Thank you for the help :))
Justin A. Lemkul, Ph.D.
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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