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

[Justin Lemkul]

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

-- 
==================================================

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
http://www.thelemkullab.com

==================================================