Approach energy with SMD (2)

From: Austin B. Yongye (ybausty_at_yahoo.com)
Date: Fri Nov 14 2008 - 13:31:36 CST

Hi everyone,
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?
Thanks,
Austin-

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.
> Thanks,
> Austin-

      

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