Hi, I haven't tried it but it should work if you set verlet-buffer-drift=-1 and set rlist manually.
Roland On Mon, Dec 2, 2013 at 3:20 PM, Brad Van Oosten <bv0...@brocku.ca> wrote: > I am trying to add virtual sites to a simulation with no mass or charge, > just > to make tracking the center of mass of groups later easier later on. > > However, I keep getting the warning "The mass of a vsiten constructing atom > is <= 0" when i run grompp. > > Here's the section of my .itp file where i have defined them: > > [ atoms ] > ; nr type resnr residue atom cgnr charge mass typeB > chargeB massB > ; residue 1 CHX rtp CHX q 0.0 > 1 CLAL 1 CHX CL1 1 -0.151 35.453 ; > qtot > -0.151 > . > . > . > . > > 63 CA 1 CHX CZ2 63 0.083 12.011 ; > qtot > 0.144 > 64 CLAL 1 CHX CL2 64 -0.144 35.453 ; > qtot > 0 > 65 MCH3 1 CHX V1 65 0 0 ; > 66 MCH3 1 CHX V2 66 0 0 ; > 67 MCH3 1 CHX V3 67 0 0 ; > 68 MCH3 1 CHX V4 68 0 0 ; > 69 MCH3 1 CHX V5 69 0 0 ; > 70 MCH3 1 CHX V6 70 0 0 ; > 71 MCH3 1 CHX V7 71 0 0 ; > 72 MCH3 1 CHX V8 72 0 0 ; > 73 MCH3 1 CHX V9 73 0 0 ; > 74 MCH3 1 CHX V10 74 0 0 ; > 75 MCH3 1 CHX V11 75 0 0 ; > 76 MCH3 1 CHX V12 76 0 0 ; > > [virtual_sitesn] > 65 2 8 9 10 11 > 66 2 2 3 6 7 > 67 2 1 4 5 12 13 > 68 2 14 15 16 17 18 > 69 2 19 20 21 22 23 > 70 2 24 25 26 27 28 29 30 31 32 > 71 2 33 34 35 36 37 38 39 40 41 > 72 2 49 50 51 52 53 > 73 2 44 45 46 47 48 > 74 2 42 43 54 57 58 > 75 2 55 56 59 60 > 76 2 61 62 63 64 > > > Am I defining something wrong here? > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Virtual-Sites-tp5012975.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.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. > > > > > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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.