Dear Justin, Thank you for your reply. I've checked it several time, and "to me" it looks fine. What exactly should be checked. Anything in particular? Best, Ali
-----Original Message----- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of Justin Lemkul Sent: vrijdag 30 november 2018 20:28 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] non-zero total charge On 11/29/18 1:13 PM, Ali Khodayari wrote: > Dear gmx community, > > > > I am getting a note before performing the energy minimization step, > from grompp that "System has non-zero charge: -0.001135". The system > is a That net charge looks somewhat large to simply be due to rounding error, so check your topology for errors. -Justin > crystalline cellulose, built in Amber, using GLYCAM06 force field and > the topology and coordinate files have been converted to gromacs > format using acpype. The system has zero charges with/without > solvation. How important is this note? Is this a large value or I can > just neglect it and continue with NVT? > > Thank you for your kind replies. > > Best > > Ali > -- ================================================== 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.