I’m using colvars to calculate the free energy of a system, I want to obtain a 1-dimensional pmf (basically the 1 reaction coordinate which distanceZ). I want to constrain the molecule, that I’m interested in getting the pmf, from wandering too much in two other direction, i.e. x and y.
Can I define two other reaction coordinates in those direction with ‘lowerWall’ and ‘upperWall’ defined for them in order to keep the molecule within the desired bound but I don’t use the in the free energy calculation part of the configuarion file? basically defining 3 reaction coordinate x, y and z but only z is used in the free energy calculations and two others defined just for keeping the molecule within the defined bound specified by their respective ‘lowerWall’ and ‘upperWall’.
I don’t know if I have to post this kind of questions here or to NAMD list?!
One more question,
If I want to confine the center of mass of the molecule between two paints along, let’s say, y axis which crosses the periodic boundary in that direction how should I define lowerWall and upperWall? for example if the box size in y direction is from -25 to 25 and initially the com of the molecule is located at y=25 but I want it to be confined in y-direction +/- 5 from its initial position. As the fix colvars use “unwrap yes” as default I thought I have to use unwrapped values as “lowerWall 20” and “upperWall 30” but I’m not positive that I understood it right?!.
I Would appreciate it if you could help me to know how I should set these values…There are also two options in the manual “period” and “wrapAround” should I also set them (i.e. “period 10” and “wrapAround 25”)? or they are not related to what I need?
PS:I read part 4.3 of “COLLECTIVE VARIABLES MODULE Reference manual for LAMMPS” release October 16, 2013, and based on my perception from that part I thought I have to use unwrapped values. By the way I’m using “distanceZ” component for this reaction coordinate (y-direction).
Ok, after more scrutinizing I managed to run it with using the “period 50” which is the length of the unit cell and “wrapAround 0.0” (basically its default value) and then I used the unwrapped values for lowerWall and upperWal…I picked these up from section 5.2.1 of “COLLECTIVE VARIABLES MODULE Reference manual for LAMMPS”…I hope I understood the idea and I’m using it right? any comment on this is well appreciated.