Dear Justin, Thank you for your answer. when I use just one chain of polymer with the protein, the charge is an integer but when I employ "insert molecules" to add more than one polymer chain, the charge will not be an integer. I am wondering what's the problem?
Best regards On Tue, Dec 3, 2019 at 4:04 PM Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/3/19 3:59 PM, SAKO MIRZAIE wrote: > > Hi All, > > I did some MD studies on a protein: polymer system. After running > grompp, > > it said, "the total charge is not an integer". the total charge is > -0.00465. > > Can I continue the MD by adding -maxwarn flag? or it will be a problem > and > > I will get unrealistic results? > > In general, it is never a good idea to use -maxwarn. > > The magnitude of that total charge is suspiciously high and you should > check your topology for proper charge assignment. > > -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 > > ================================================== > > -- *********************************************** Sako Mirzaie Sako Mirzaie Ph.D. in biochemistry, Assistant Professor, Science Faculty, Islamic Azad University of Sanandaj, Sanandaj, Iran Visiting Professor, Advanced Pharmaceutics & Drug Delivery Laboratory Leslie Dan Faculty of Pharmacy University of Toronto 144 College Street, Toronto, Ontario Canada M5S 3M2 http://scholar.google.com/citations?user=viwZvVAAAAAJ&hl=en http://www.scopus.com/authid/detail.url?authorId=54886431500 http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie https://www.researchgate.net/profile/Sako_Mirzaie/publications/ -- 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.