[gmx-users] Constraining hydrogen - heavy atom bonds with different naming.

Justin Lemkul jalemkul at vt.edu
Tue Mar 1 19:29:53 CET 2016

On 3/1/16 1:24 PM, Dawid das wrote:
> Dear Gromacs Experts,
> I am pretty sure I have already answered this question long time ago but I
> cannot find
> it. What I did is I added a new residue for my system and it contains
> hydrogen atoms.
> Now, the thing is that all atoms names start with "M", so I have MH21,
> MH22, MCA1, etc.
> atoms. I want to constrain hydrogen - heavy atom bonds:
> constraints   = h-bonds
> and I am not sure whether I constraint those novel hydrogens.  In other
> words, how does
> Gromacs 5.0.4 know that my atom is a hydrogen? Based on atomic number in
> ffnonbonded.itp or based on atom name/type?

It's based on name.  If the first character is H, it is added to the constraint 
list.  So your case will not work.  You can always confirm what is constrained 
by using gmx dump on the .tpr file and looking for F_CONSTR.



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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