[gmx-users] periodic molecule
Justin Lemkul
jalemkul at vt.edu
Wed Sep 18 13:49:18 CEST 2013
On 9/18/13 5:42 AM, Valentina wrote:
> 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?!
>
That's one possibility, and it may be worth trying. From the movie, it appears
that al2 and al3 are trying to bond with one another within the unit cell, not
across PBC. Theoretically, either approach should work, since the distance
between the atoms is all that should matter.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
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
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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