> > > On 4/27/14, 4:25 PM, Nilesh Dhumal wrote: >>> >>> On 4/27/14, 4:01 PM, Nilesh Dhumal wrote: >>>> Hello, >>>> >>>> I run g_dipoles for two different systems (System are ionic liquids). >>>> >>>> For one system when I run g_dipoles I get following message >>>> >>>> There are 256 molecules in the selection >>>> There are 256 charged molecules in the selection, >>>> will subtract their charge at their center of mass >>>> >>>> >>>> and I don't get this message for other system. >>>> >>>> Why program subtract their charge at their center of mass for one >>>> system >>>> and not for other. >>>> >>> >>> Based on whatever the topology says, g_dipoles doesn't find a net >>> charge >>> on >>> whatever these molecules are. Without providing more information - >>> what >>> the >>> molecules/selections are, what the topology(ies) is(are) - that's all >>> that >>> can >>> be surmised at this point. >>> >>> -Justin >>> >> >> There are 128 cations (EMI) and 128 anions (ETS). Total charge is ZERO >> >> here is molecular section from topology file. >> [ defaults ] >> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ >> 1 3 yes 0.5 0.5 >> >> #include "emi.itp" >> #include "ets.itp" >> >> >> [ molecules ] >> ; Compound #mols >> EMI 128 >> ETS 128 >>
For other system I have different anion. I didn't specify the number of residues in molecular section. [ system ] ; Name Grunge ROck MAChoS t= 20000.00000 [ molecules ] ; Compound #mols Ion 1 Nilesh > > You said you had two different systems. What's the difference between > them? > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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.