[gmx-users] bonded interaction larger than cutoff
Quyen Vu Van
vuqv.phys at gmail.com
Tue Dec 18 10:11:47 CET 2018
Thanks Dr. Lumkel
On Mon, Dec 17, 2018 at 2:30 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> On Mon, Dec 17, 2018 at 7:48 AM Quyen Vu Van <vuqv.phys at gmail.com> wrote:
> > Dear all,
> > I add a harmonic bond between two ends of my molecule (then my molecule
> > will have circle shape) with hope to calculate the force opens my
> > (force the molecule straight).
> > Unfortunately, when this bond is quite big, gromacs said this bonded
> > interaction could not be calculated.
> > How can I overcome this? or is there any setup to calculate
> Either do not use domain decomposition or use the pull code to bias the
> distance rather than trying to use a formal covalent bond.
> 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
> jalemkul at vt.edu | (540) 231-3129
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * 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-request at gromacs.org.
More information about the gromacs.org_gmx-users