On Sun, Jun 9, 2013 at 5:06 AM, <moitrayee.mbu.iisc.ernet.in> wrote:
> Dear Amber Users,
> I am planning to run an SMD calculation using ncsu_smd usinf Amber12. After
> reading the manual and the related Amber posts, I am still confused that
> whether
> if I want to push an atom near another atom by 10angstroms, both the atoms
> will
> move. Is it possible to fix the coordinate of one and move just the other
> atom
> relative to the fixed atom?
>
Sure, I could think of 2 ways off the top of my head to accomplish this.
You could use cartesian restraints on the atom you want to fix to keep it
from moving very far, or you could increase the mass of atom you want to
fix so it's basically too heavy to move. In either case, I would question
the motive -- what's your reason for wanting to fix one atom? I can't
think of any advantages of doing SMD this way... You may have a hard time
defending these approaches if/when you seek to publish your work.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jun 10 2013 - 21:30:03 PDT
