On 10/7/19 10:40 PM, 张 卓 wrote:
Dear Justin, I have tried implicit solvent without pbc or barostat. The box was not compressed but the molecules flew out of the box. I believe that it was because of nopbc box. Would you please give more information on why implicit solvent is used without pbc?
Because there's no need for it. In explicit solvent simulations, we use PME for long-range electrostatics and that requires PBC. In implicit solvent, there's no need (this is also a reason why implicit simulations have intrinsic accuracy issues).
Beyond that, regarding your observations, there is no box. The molecule is simply diffusing through space, which will happen in any simulation. In a simulation with PBC, this has the effect of the molecule crossing back and forth over borders ("jumping"), which simply doesn't happen in your case.
-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.
