Update
https://docs.google.com/file/d/0B6Qm4snFANimcmxYVnBOSkNCd2s/edit?usp=sharing
Seems I had to declare the atoms in .rtp with + and - when they are across
periodic boundary.
The new movie is showing that atoms do move, but not across the box. Yes, I
would have to play a little ore with parameters for the system (ongoing
work), but the major problem with PBC is sorted.
I am giving below my new (working) molecule.rtp file, that is different from
the earlier one - may be once this it may be helpful for someone;)
Thanks!
[ 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
al3 +o1 b_ac-oc
al3 +o2 b_ac-oc
al3 +o3 b_ac-oc
o4 al1 b_ac-oc
o5 al1 b_ac-oc
o6 al1 b_ac-oc
al2 -o7 b_ac-oc
al2 -o8 b_ac-oc
o9 al1 b_ac-oc
o10 al1 b_ac-oc
o11 al1 b_ac-oc
o12 al2 b_ac-oc
al2 -o13 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
--
View this message in context:
http://gromacs.5086.x6.nabble.com/periodic-molecule-tp5011270p5011291.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
