On 11/26/18 12:01 AM, Karpurmanjari Kakati wrote:
Dear All, My System contains, while doing NVT of the same, I got the following Note *NOTE 1 [file sa.top, line 80]: System has non-zero total charge: 12.936997 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic <http://www.gromacs.org/Documentation/Floating_Point_Arithmetic> for discussion on how close it should be to an integer.* This is possibly because of the partial charges in the molecules in the ITP fie.
Something isn't parametrized correctly because you need to have an integer charge. Your total charge is not physical.
-Justin
My doubt is can't I have a system with non zero and a decimal charge value. Also I got the following warning: *WARNING 1 [file sa.top, line 80]: You are using Ewald electrostatics in a system with net charge. This can lead to severe artifacts, such as ions moving into regions with low dielectric, due to the uniform background charge. We suggest to neutralize your system with counter ions, possibly in combination with a physiological salt concentration.* Can Someone help me with this? Also this : *Velocities were taken from a Maxwell distribution at 300 KRemoving all charge groups because cutoff-scheme=VerletAnalysing residue names:There are: 1 Other residuesThere are: 100000 Water residues* Removing all charge group because the cut off scheme is verlet. If That happens then will it show the behavior I want to see. Or shall I put any other scheme on that ? Please help
-- ================================================== 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.
