Dear amber users,
I am trying to restrain an ion in x and z coordinates and so letting it
move only in y direction, such that when I apply steered molecular dynamics
to pull the ion in/out, it only moves in y direction (essentially, I want
to drag the ion in y coordinate into the protein).
I have read some of the previous questions on this:
http://archive.ambermd.org/201406/0378.html
http://archive.ambermd.org/201405/0596.html
My question is that,
1) After modifying the constraint file, all other restraints will also be
applied in x and z only - I don't want this! Because my other restraints
should be in xyz, how can this be solved?
2) Does this modification apply to nmr type restraint (nmropt=1) or
positional restraint (ntr=1)? or both?
3) Also, can I do this in pmemd.cuda?
Thanks much for your help,
Samantha
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Received on Wed Apr 29 2015 - 21:00:02 PDT
