[gmx-users] Deuterium atoms

[Justin Lemkul]

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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