[gmx-users] Deuterium atoms

[Justin Lemkul]

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
>>>>>>
>>>>>
>>>>
>>>
>>
>

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

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