Hello! I have a surface, formed by Mg2Al(OH)6.
All of the O are bonded with Al, by such forming a mesh. I am using periodic_molecule=yes as discussed in this thread: http://gromacs.5086.x6.nabble.com/generating-user-defined-topologies-for-surfaces-td5010192.html#a5010234 I set up the topology for the small unit shown in blue frame on this picture - http://gromacs.5086.x6.nabble.com/file/n5010233/Screen_Shot_2013-07-31_at_13.41.17.png Then I make a big layered structure of 4 x 4 x 4 of such units and do energy minimisation, using following script: integrator = steep nsteps = 5000 emtol = 10 emstep = 0.01 nstxout = 1 nstenergy = 1 rlist = 1.0 pbc = xyz periodic_molecules = yes coulombtype = PME rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 And my Al that had bonds across periodic system (al2 and al3) move - see movie: https://docs.google.com/file/d/0B6Qm4snFANimRXZ3QTlVQ1J0MlE/edit?usp=sharing Colour coding: al2 is shown as large cyan and al3 is shown as large blue. al1 is shown in small cyan - it's the only al that does not do a big move. all mg are shown in pink I am not sure - have I set up periodic molecule wrong? My molecule.rtp for the using looks like: [ bondedtypes ] ; bonds angles dihedrals impropers 1 1 0 0 [ B21 ] ;# ldh21 [ atoms ] ; atomname atomtype charge chargegroup o1 oc18 -0.875 3 h1 hoy 0.350 3 o2 oc17 -0.875 3 h2 hoy 0.350 3 o3 oc20 -0.875 3 h3 hoy 0.350 3 o4 oc21 -0.875 1 h4 hoy 0.350 1 o5 oc16 -0.875 1 h5 hoy 0.350 1 o6 oc19 -0.875 1 h6 hoy 0.350 1 mg1 mg 1.40 0 al1 ac3 1.35 1 mg2 mg 1.40 0 o7 oc16 -0.875 2 h7 hoy 0.350 2 o8 oc19 -0.875 2 h8 hoy 0.350 2 o9 oc18 -0.875 1 h9 hoy 0.350 1 o10 oc17 -0.875 1 h10 hoy 0.350 1 o11 oc20 -0.875 1 h11 hoy 0.350 1 o12 oc21 -0.875 2 h12 hoy 0.350 2 mg3 mg 1.40 0 mg4 mg 1.40 0 al2 ac3 1.35 2 o13 oc20 -0.875 2 h13 hoy 0.350 2 o14 oc21 -0.875 3 h14 hoy 0.350 3 o15 oc16 -0.875 3 h15 hoy 0.350 3 o16 oc19 -0.875 3 h16 hoy 0.350 3 o17 oc18 -0.875 2 h17 hoy 0.350 2 o18 oc17 -0.875 2 h18 hoy 0.350 2 al3 ac3 1.35 3 mg5 mg 1.40 0 mg6 mg 1.40 0 [ bonds ] ; atom1 atom2 parametersindex o1 h1 b_oc-h o2 h2 b_oc-h o3 h3 b_oc-h o4 h4 b_oc-h o5 h5 b_oc-h o6 h6 b_oc-h o7 h7 b_oc-h o8 h8 b_oc-h o9 h9 b_oc-h o10 h10 b_oc-h o11 h11 b_oc-h o12 h12 b_oc-h o13 h13 b_oc-h o14 h14 b_oc-h o15 h15 b_oc-h o16 h16 b_oc-h o17 h17 b_oc-h o18 h18 b_oc-h o1 al3 b_ac-oc o2 al3 b_ac-oc o3 al3 b_ac-oc o4 al1 b_ac-oc o5 al1 b_ac-oc o6 al1 b_ac-oc o7 al2 b_ac-oc o8 al2 b_ac-oc o9 al1 b_ac-oc o10 al1 b_ac-oc o11 al1 b_ac-oc o12 al2 b_ac-oc o13 al2 b_ac-oc o14 al3 b_ac-oc o15 al3 b_ac-oc o16 al3 b_ac-oc o17 al2 b_ac-oc o18 al2 b_ac-oc [ angles ] ; ai aj ak gromos type al3 o14 h14 a_ac-oc-h al3 o15 h15 a_ac-oc-h al3 o1 h1 a_ac-oc-h al3 o16 h16 a_ac-oc-h al3 o2 h2 a_ac-oc-h al3 o3 h3 a_ac-oc-h al1 o4 h4 a_ac-oc-h al1 o5 h5 a_ac-oc-h al1 o9 h9 a_ac-oc-h al1 o6 h6 a_ac-oc-h al1 o10 h10 a_ac-oc-h al1 o11 h11 a_ac-oc-h al2 o12 h12 a_ac-oc-h al2 o7 h7 a_ac-oc-h al2 o17 h17 a_ac-oc-h al2 o8 h8 a_ac-oc-h al2 o18 h18 a_ac-oc-h al2 o13 h13 a_ac-oc-h o5 al1 o10 a_oc-ac-oc_1 o7 al2 o18 a_oc-ac-oc_1 o15 al3 o2 a_oc-ac-oc_1 o9 al1 o6 a_oc-ac-oc_1 o17 al2 o8 a_oc-ac-oc_1 o1 al3 o16 a_oc-ac-oc_1 o11 al1 o4 a_oc-ac-oc_1 o13 al2 o12 a_oc-ac-oc_1 o3 al3 o14 a_oc-ac-oc_1 o5 al1 o9 a_oc-ac-oc_2 o7 al2 o17 a_oc-ac-oc_2 o15 al3 o1 a_oc-ac-oc_2 o5 al1 o4 a_oc-ac-oc_2 o7 al2 o12 a_oc-ac-oc_2 o15 al3 o14 a_oc-ac-oc_2 o10 al1 o6 a_oc-ac-oc_2 o18 al2 o8 a_oc-ac-oc_2 o2 al3 o16 a_oc-ac-oc_2 o10 al1 o11 a_oc-ac-oc_2 o18 al2 o13 a_oc-ac-oc_2 o2 al3 o3 a_oc-ac-oc_2 o9 al1 o4 a_oc-ac-oc_2 o17 al2 o12 a_oc-ac-oc_2 o1 al3 o14 a_oc-ac-oc_2 o6 al1 o11 a_oc-ac-oc_2 o8 al2 o13 a_oc-ac-oc_2 o16 al3 o3 a_oc-ac-oc_2 o5 al1 o6 a_oc-ac-oc_3 o7 al2 o8 a_oc-ac-oc_3 o15 al3 o16 a_oc-ac-oc_3 o5 al1 o11 a_oc-ac-oc_3 o7 al2 o13 a_oc-ac-oc_3 o15 al3 o3 a_oc-ac-oc_3 o10 al1 o9 a_oc-ac-oc_3 o18 al2 o17 a_oc-ac-oc_3 o2 al3 o1 a_oc-ac-oc_3 o10 al1 o4 a_oc-ac-oc_3 o18 al2 o12 a_oc-ac-oc_3 o2 al3 o14 a_oc-ac-oc_3 o9 al1 o11 a_oc-ac-oc_3 o17 al2 o13 a_oc-ac-oc_3 o1 al3 o3 a_oc-ac-oc_3 o6 al1 o4 a_oc-ac-oc_3 o8 al2 o12 a_oc-ac-oc_3 o16 al3 o14 a_oc-ac-oc_3 Where al2 and al3 have bonds (and angles) across periodic bond. Have I done a mistake in a set up? Shall I rather have a specbond file?! Thank you for help! V -- View this message in context: http://gromacs.5086.x6.nabble.com/periodic-molecule-tp5011270.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists