[gmx-users] Deuterium atoms

Justin Lemkul jalemkul at vt.edu
Thu Jun 21 14:17:12 CEST 2018

On 6/21/18 3:47 AM, Hermann, Johannes wrote:
> Thanks Vytautas, might solve it! And additionally change the mass in 
> the force field.

Increasing the mass will also change the vibrational frequency of any 
bonds involved, requiring a reparametrization of the bonded force 
constant. If you're using constraints, this does not matter, but then I 
sort of wonder why you're bothering to replace H with D and expect to 
see any kind of difference.


> On 21.06.2018 09:24, Vytautas Rakeviius wrote:
>> Just change all D to H in structure file IMHO.
>>      On Wednesday, June 20, 2018, 5:39:18 PM GMT+3, Hermann, Johannes 
>> <J.Hermann at lrz.tu-muenchen.de> wrote:
>>     Dear all,
>> is there any force field in gromacs (or elsewhere) which can handle
>> deuterium atoms?
>> All the best
>> Johannes


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

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