From: Austin B. Yongye (ybausty_at_yahoo.com)
Date: Mon Nov 03 2008 - 11:01:26 CST
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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