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-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: Thursday, June 21, 2018 9:09 AM To: gmx-us...@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.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 >>>>>> >>>>> >>>> >>> >> > -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.