Hi,
I am attempting to run a steered MD simulation (using sander with
ncsu_smd) where I pull on a loop of the protein in a given direction.
I figure using a DISTANCE variable is the easiest way to do this, but
unfortunately there are no two atoms that are lined up in the
direction that I would like to pull. Therefore, I would like to add a
dummy atom so that I can pull the protein loop in the direction of the
dummy atom.
Based on a previous thread on the list, I added a dummy atom by adding
an ion to my protein and then editing the ion parameters (with parmed)
to set the VDW, charge and GB Radii and Screen terms to 0.0. However,
when the GB Radii and Screen terms are zero the overall energy is
always "NaN". If I only change the VDW and charge parameters, my dummy
atom still interacts with the environment (I am using implicit
solvent) and slowly moves away from the protein during the simulation.
My current solution is to restrain the movement of the dummy atom so
that it cannot move away from the protein, however this is non-ideal.
I assume that another solution would be to use explicit solvent,
although I would prefer to stick with implicit solvent. Is there
another way to use a dummy atom with implicit solvent? Alternatively,
is there a better way to pull the protein in a specific direction
without the addition of a dummy atom?
Thank you,
Kyle
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Received on Tue Jan 22 2013 - 08:00:02 PST
