[gmx-users] Deuterate organic solvent

Justin Lemkul 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.
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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