[gmx-users] Heavy Hydrogens

Matthew Harrigan harrigan at stanford.edu
Thu Apr 23 23:41:53 CEST 2015

Hi Justin, 
I was thinking of doing that. I'll have to be careful about removing mass from the (correct) attached atoms to preserve the total mass of the system 

----- Original Message -----

From: "Justin Lemkul" <jalemkul at vt.edu> 
To: gmx-users at gromacs.org 
Sent: Thursday, April 23, 2015 2:39:20 PM 
Subject: Re: [gmx-users] Heavy Hydrogens 

On 4/23/15 4:25 PM, Matthew Harrigan wrote: 
> Hi all, 
> There is an option in pdb2gmx "-heavyh" which shuffles some mass from the connected heavy atom to the hydrogen. I want to do this, but starting from a top, gro pair of files. Specifically, I don't want gromacs to try to regenerate all the forcefield parameters in my top file. Does anyone have suggestions for how I can go about this? 

Write a simple parser that modifies the listed masses in [atoms]. This should 
be straightforward in something like Perl or Python. 



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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