[gmx-users] periodic molecule

Valentina valentina.erastova at durham.ac.uk
Wed Sep 18 11:42:12 CEST 2013


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:

I set up the topology for the small unit shown in blue frame on this picture

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

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!

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