From: Alex Liu (liu.alex77_at_yahoo.com)
Date: Thu Jan 06 2011 - 15:46:14 CST
Dear NAMD users,
I want to move an ion along z axis using dynamic z axis as explained in
component "distanceZ" in NAMD 2.7b3 and get the PMF profile using ABF.
I also want to confine the ion movement in XY plane so, I am using component
"distanceXY" and for both components I am defining "main", "ref" and "ref2".
In addition to above, I want to fix both ends of the dynamic z axis (using a
force constant) by fixing the atoms I am using to define this axis (the
atom numbers I have already used to define "ref" and "ref2"), but I am not sure
whether I am doing it correct or not. Here is what I do:
I define 6 colvars:
Clovars1 and 2 are for the ion movement:
Colvar 1. distanceZ to define the dynamic Z axis for the ion pathway (main, ref,
ref2). Here main is the atom number of ion.
Colvar 2. distanceXY to confine the ion movement in XY plane (main, ref,
ref2). Here main is the atom number of ion above.
Colvars 3 and 4 are for fixing the ref atoms:
Colvar3. distanceZ (main, ref, ref2). Here main is the same as ref in terms of
the atom selection so, one end of the dynamic axis is fixed in Z direction.
Colvar4. distanceXY (main, ref, ref2). Here main is the same as ref in terms of
the atom selection so, one end of the dynamic axis is fixed in XY plane.
Colvars 5 and 6 are for fixing the ref atoms:
Colvar5. distanceZ (main, ref, ref2). Here main is the same as ref2 in terms of
the atom selection so the other end of dynamic axis is fixed in Z direction.
Colvar6. distanceXY (main, ref, ref2). Here main is the same as ref2 in terms
of the atom selection so the other end of the dynamic axis is fixed in XY plane.
Then to get the PMF profile for ion movement (1-D) I just need to define Colvar
1 in ABF part. Can anyone please tell me if this approach is correct?
In NAMD 2.6, I did this by using something like below:
constraints on
consRef restrain_ion.pdb
consKFile restrain_ion.pdb
consKCol o
selectConstraints on
selectConstrX on
selectConstrY on
selectConstrZ on
So, I was thinking maybe instead of defining Colvars 3-6 in colvars
configuration file to fix the atoms at both ends of the dynamic axis, I can
simply use commands above in namd configuration file and just define Colvars 1
and 2 for the ion movement in colvars configuartion file. Is this also true?
Or does anyone know another method I can use to fix these atoms?
Thanks a lot for your time,
Alex
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