Oh thank you very much I think I got confused looking at older documentation.
What sort of artefacts get created by using comm-grps = Protein non-Protein? On Wed, Feb 5, 2020 at 11:14 PM Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 2/3/20 7:33 PM, Miro Astore wrote: > > Hi everyone, > > > > I have tried using comm_grps to try and remove center of mass motion > > from my system. > > > > I used the following configuration > > > > comm_grps = non-Protein Protein > > nstcomm = 100 > > comm_mode = linear > > comm_grps = non-Protein Protein > > Don't do this. Multiple COM motion removal groups are only appropriate > in layered systems that have different diffusion behavior. > > > > refcoord_scaling = com > > > > But I still get considerable drift in my protein. Am I > > misunderstanding what comm is actually doing and I should use the > > pulling code if I want my protein to stay in the center of the box? > > Dallas covered this nicely. The algorithm does not (and is not intended > to) prevent diffusion. It subtracts erroneous contributions to the > kinetic energy in the system. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 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.
