Vijayaraj wrote:
Hello,
I am doing umbrella sampling to calculate PMF curve for the detachment
of a terminal cyclic peptide with 8 aa's (CP) from the self-assembled
cyclic peptide nanotube. I extracted the reaction coordinates staring
from 5.5 ang COM distance between the terminal CP and the 2nd CP to 17.5
ang, I did umbrella sampling on 25 configurations (for 5ns) and the
window size is 0.5 ang. I used the following pulling code for umbrella
sampling,
pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = yes
pull_ngroups = 1
pull_group0 = Chain_B
pull_group1 = Chain_A
pull_init1 = 0
pull_rate1 = 0.0
pull_k1 = 1000
pull_nstxout = 1000
pull_nstfout = 1000
I restrained the 2nd CP unit and the pull_rate1 is 0, so the COM
distance between the chain_A (terminal) and chain_B (2nd CP) should be
restrained. after 5ns of umbrella sampling, I calculated the COM
distance between chain A and B, but it was not restrained, for the 5.5
ang COM distance restrain, the COM distance varies from 4.5 to 5.5 ang.
and also the pulling cyclic peptide undergoes large conformational
sampling. from the WHAM analysis I understood the sampling window is
poorly represented. In addition to COM distance restrain, can I restrain
the pulling CP's backbone atoms? so that the pulling groups large
conformational sampling will be reduced.
You could implement dihedral restraints to fix the backbone secondary structure,
but I can't comment on the stability of trying to use these restraints in
addition to the pull code. Seems like a lot going on at once, to me.
Also consider the fact that 5 ns is an extremely short timeframe to gather
meaningful data. Perhaps you just need more time in each window to equilibrate.
At the shortest COM distance, your two molecules are still likely experiencing
some interactions, and it may require a great deal of sampling in this window to
converge the simulations. You haven't shown the rest of your .mdp file (always
a good idea!), so we can only guess at whether or not your other settings should
lead to a sensible result.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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