From: Jeff Forbes (forbesj_at_mail.nih.gov)
Date: Wed Apr 23 2008 - 14:36:16 CDT
I have performed a constant velocity SMD of a protein with
a velocity of 0.000005A/step. I would now like to push the
SMD atom back towards its original position at the same velocity.
Simply changing the sign of the SMDDir parameter does not work as expected.
The SMD atom moves in the correct direction, but the velocity is much
faster than expected.
The original position of the SMD atom is reached in ~ 70 ps, where as
the stretched starting position was reached
after ~42 ns. The average reverse velocity is ~ 3e-3A/step, quite a
Any suggestion on how to get the expected behavior would be welcomed.
Jeffrey G. Forbes, Ph.D.
Muscle Proteomics and Nanotechnology Section
Laboratory of Muscle Biology
National Institute of Arthritis and
Musculoskeletal and Skin Diseases
National Institutes of Health
Department of Health and Human Services
50 South Drive
Building 50, Room 1139
Bethesda, MD 20892-8024
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