You already are. The [position_restraints] directive is applied to the
atom(s) of the [moleculetype] that >contains it, so if you only have one
[moleculetype] then any instance of it will have the restraint >applied
to whatever atoms are indicated.
-Justin
Hi Justin, thanks for your reply.
If this is the case then should I not expect to see all the position
restraints in the .tpr file?
Using gmxdump -s md1.tpr to inspect the file I can only see
Position Rest.:
nr: 2
iatoms:
0 type=1 (POSRES) 0
(this is on the simplified 5 atom case). Which implies there is one
position restraint on atom 1 (index 0 I guess).
Craig
Craig Kitchen wrote: Dear All, My system consists of 32 identical molecules
(with 91 atoms per molecule). I would like to apply a position restraint to
the 91st atom of each molecules. Since all my molecules are identical I
only have one [moleculetype] which contains 91 atoms. I have defined
-DPOSRES in the .mdp file and have placed: #ifdef POSRES #include
"posre.itp" #endif in (hopefully) the correct part of the topology file
(immediately below the only [moleculetype]). There are no solvent molecules
or ions. Applying a position restraint to atom 91 works fine with posre.itp
containing: [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000
2000 2000 This results in just one restraint to atom 91. But if I want to
restrain the 91st atom in the second molecule (atom 182 in the .gro file),
how do I do it?
You already are. The [position_restraints] directive is applied to the
atom(s) of the [moleculetype] that contains it, so if you only have one
[moleculetype] then any instance of it will have the restraint applied to
whatever atoms are indicated.
-Justin
[ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000
182 1 2000 2000 2000 Does not work since 182 is outside the atom numbers in
the [moleculetype] (1 to 91). Similarly, having 32 lines in posre.itp
reading "91 1 2000 2000 2000" gives 32 position restraints to atom 91. I
expect I can get around this problem by duplicating the current topology 32
times and creating a huge topol.top file with all 2912 atoms defined
explicitly. However, it seems there should be a more elegant way to achieve
this. Any help would be greatly appreciated! I have included below a
simplified example with all the other atoms removed. In this case, how do
you restrain the position of atom 2,3,4 and 5? Craig Craig Kitchen
Department of Chemistry University of Cambridge Lensfield Road Cambridge
CB2 1EW UK topol.top: [ moleculetype ] ; Atom ; Name nrexcl UNK 3 [ atoms ]
; nr type resnr resid atom cgnr charge mass
1 amber99_41 1 UNK OAI 1 -0.50762 15.9994
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
[ system ]
; Name
Multiple Atoms
[ molecules ]
; Compound #mols
UNK 5
Starting conf.gro:
Multiple Atoms
5
1UNK OAI 1 0.767 1.527 0.970
2UNK OAI 2 0.988 0.716 1.774
3UNK OAI 3 0.556 0.587 0.434
4UNK OAI 4 0.335 1.656 2.436
5UNK OAI 5 0.766 1.527 2.373
2.64620 3.76260 2.80720
File used for restraint coordinates (grompp -r) :
Restraint coordinates
5
1UNK OAI 1 0.000 1.500 1.000
2UNK OAI 2 1.100 0.621 2.000
3UNK OAI 3 0.399 0.621 0.349
4UNK OAI 4 0.221 1.562 -0.343
5UNK OAI 5 0.923 1.561 2.458
2.64620 3.76260 2.80720
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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