Amberites,
I have already gotten some very good advice to apply to the NSF for
computational resources to carry out Nudged Elastic Band simulations to
determine the reaction coordinates and energy barrier of a large
conformational change in an RNA. In the meantime, I do now want this project
to stagnate, so I am looking for advice on alternatives. I have been reading
the manual and I think that Steered MD and umbrella sampling would be great,
but they appear to require information about the pathway between the
conformations. I can make some educated guesses about this pathway, based on
sugar puckers, dihedral angles, etc; however, the conformational change
would require many residues to undergo many different changes at the same
time.
Targeted MD seems to be the most ideal method that I have found. I would
like to perform this simulation on my system, but I wanted some expert
advice on the caveats of this method.
1. Does the reference structure need to have the same number of atoms
(including solvent) even if the number and names of the atoms in the masks
are the same?
2. I assume that it is standard practice to perform standard minimization
and equilibration prior to TMD. Should these be performed multiple times to
achieve a better representation of the error associated with the method?
3. Assuming that weight changing is used to gradually lower the target RMSD
value over the course of the simulations, does a longer simulation (say 10ns
vs. 20ns) translate to a more accurate representation of the path?
I would also be open to any other advice that you think may be helpful.
Thank you in advance. I look forward to learning more.
Adieu,
Will
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Received on Mon Oct 03 2011 - 18:00:03 PDT
