[gmx-users] Position restraints with multiple identical molecules

[Craig Kitchen]

> 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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