[gmx-users] How to change to heavyh in an equilibrated system

Justin Lemkul jalemkul at vt.edu
Fri Jul 6 13:46:56 CEST 2018

On 7/6/18 4:52 AM, Ramon Crehuet wrote:
> Dear all,
> For testing reasons, I would like to compare a system that I have setup using heavy hydrogens (-heavyh option in pdb2gmx) to exactly the same system without using heavy hydrogens.
> I could redo all the system setup starting from the pdb2gmx, but I would like to avoid that. That setup was tedious and I would like to start from the exactly the same coordinate file.
> I could write a script to change the atom masses in the .itp files, but again, this doesn't seem the easiest way.
> Is there a way to generate a new topology from the equilibrated .gro or .tpr file? (when simply feeding these files to pdb2gmx the ions are not recognized).

If you only want to introduce a difference in the topology, re-process 
the starting coordinates (protein or whatever) with pdb2gmx and then 
just update the .top to match the contents of the non-heavy H system. 
The coordinates will be the same but the topology will be different.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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