[gmx-users] Deuterium atoms

[Smith, Micholas D.]

Typically, deuterium is treated with the same parameters as H, but with double the mass. Most papers don't even bother with the re-parameterization, using the argument that the bond-lengths will not change substantially. Instead the authors focus on how the dynamics are slowed. 

If you really want to use deuterium properly you should consider re-parameterizing, but it really boils down to what phenomena you are most interested in looking at? Which begs the question, why are you using D instead of H? Are you trying to match an experiment that had deuterurated samples?

As an aside, If this is extremely low-temp or related to proton tunneling then you may also need to consider not doing traditional MD, but instead Ring-Polymer MD (i.e. Path Integral Molecular Dynamics), because the BO approximation may not applicable. But then you can't use gromacs for that...

===================
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Thursday, June 21, 2018 9:09 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Deuterium atoms

On 6/21/18 9:05 AM, Hermann, Johannes wrote:
> Hello Justin,
>
> okay that is beyond my expertise. Do you know / think if there will be
> a force field in the future where deuterium is present?
>

There are tons of published studies that have done MD with deuterium. I
suggest you start there.

-Justin

> All the best
>
> Johannes
>
>
> On 21.06.2018 15:01, Justin Lemkul wrote:
>>
>>
>> On 6/21/18 8:53 AM, Hermann, Johannes wrote:
>>> Hello Justin,
>>>
>>> thank you for your answer. So the only way to simulate with
>>> deuterium atoms would be a parametrization of the force field, in
>>> particular the bonded force constant?
>>>
>>
>> At minimum. All parameters are connected, so angles and dihedrals may
>> be affected by different vibrational frequencies.
>>
>> -Justin
>>
>>> Thank you in advance!
>>>
>>> All the best
>>>
>>> Johannes
>>>
>>>
>>> On 21.06.2018 14:16, Justin Lemkul wrote:
>>>>
>>>>
>>>> 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.
>>>>
>>>> -Justin
>>>>
>>>>> 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

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

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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

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