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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