[gmx-users] umbrella sampling

Vijayaraj vijayaraj81 at gmail.com
Fri Oct 28 13:32:04 CEST 2011


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.
I am using gromacs 4.5.5 version.
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