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.herm...@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.
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Virginia Tech Department of Biochemistry
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