[gmx-users] Position restraints with multiple identical molecules

[Justin A. Lemkul]

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

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