From: Austin B. Yongye (ybausty_at_yahoo.com)
Date: Fri Nov 14 2008 - 13:31:36 CST
I sent out the email below ~1.5wks ago and haven't received a response. Finally, I have settled on doing a constant velocity pulling SMD simulation. Meanwhile, I have looked at a lot of publications that employed SMD, and noticed that they typically involve protein unfolding or ligand extraction.
Questions: has anyone ever employed SMD to pull together two atoms in a protein? Was the SMD tool intended for such use?
PS. Needless to say all attempts to pull together the two termini in my peptide have led to the peptide being pulled apart.
> Hi everyone,
> I am trying to pull together the two ends of a linear
> peptide in order to determine the energies of specific
> points on the approach trajectory. I would like to vary the
> separation distance in 1-Angstrom steps, equilibrate the
> system for say x picoseconds, carry out production dynamics
> for another y picoseconds and determine the average energy
> at the given separation distance, until the distance between
> the two atoms is 1.335A.
> I have read the SMD section of the manual, and can't
> figure out how to equilibrate and run production dynamics at
> specified distances. I am currently thinking of using the
> SMDVel parameter to change the separation distances within a
> given time interval (e.g. 2Angs/50ps) and then get the
> energy changes in 50-ps bins. Any suggestions will be
> greatly appreciated.
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