[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

==================================================



More information about the gromacs.org_gmx-users mailing list