From: Hannah Scott (hrs00003_at_mix.wvu.edu)
Date: Thu Dec 09 2021 - 14:42:28 CST
I am seeing an unusually high force being applied in the wrong direction
when applying constant velocity steered MD to my system. For this
simulation I am applying SMD to a single alpha-carbon in a helical peptide
and pulling along the -z axis in an attempt to simulate insertion into a
membrane bilayer with a 1 fs timestep.
When visualizing my system, I see that the peptide is being pulled in
the +z direction instead. The SMD output shows that the initial force
applied is very large. What could be causing this and what do you
recommend I try?
The following are the parameters I have set for the SMD simulation as well
as the output:
SMD on
SMDFile ../current-parameters/rev-smd.ref ;# this is the pbd file with
b-column needs remade with different systems
SMDk 10 ;#adjusted to pull on termius of
phlip
SMDVel .00001 ;# 10 A/ns = .01 A/ps = .00001 A/fs
SMDDir 0 0 -1
SMDOutputFreq 100
SMD 0 5.801 -4.258 27.644 0 -0 27336.5
SMD 100 6.09131 -4.67441 31.9466 0 -0 24346.4
SMD 200 6.91383 -3.83161 34.0325 0 -0 22896.4
SMD 300 7.37256 -3.92352 36.4932 0 -0 21186.1
SMD 400 7.21118 -4.2608 39.8742 0 -0 18836.3
SMD 500 6.8234 -3.46171 43.0824 0 -0 16606.6
SMD 600 6.92947 -2.77978 46.19 0 -0 14446.8
SMD 700 7.27499 -2.5372 48.6056 0 -0 12767.7
SMD 800 8.21247 -2.39816 50.8552 0 -0 11204
SMD 900 8.02797 -1.72661 53.5881 0 -0 9304.52
SMD 1000 7.32698 -1.27389 55.6482 0 -0 7872.5
Thank you in advance,
Hannah
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