[gmx-users] Position restraints with multiple identical molecules

[Craig Kitchen]

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?

[ 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