[gmx-users] Number of windows in umbrella sampling

shahid nayeem msnayeem at gmail.com
Mon Feb 13 12:21:08 CET 2012

Dear Justin
I am doing umbrella pulling simulation of a protein complex wt and mutant.
I expect mutant to give lower deltG value. I am attaching a tif file of
energy vs time curve of wt and mutant protein on pulling simulation. These
energies are obtained by g_energy and selecting 11 option which is COM
pulling energy. In this curve the first peak decreases and again rises at
longer time. How many windows should be selected. As expected the peak of
COM pulling energy is lower in mutants. Please explain why the energy again
rises at higher time. Should I use the windows upto 160ps only because
thereafter in both curve there is rise in energy value. the pull code used
is as follows.

pull_geometry   = distance
pull_dim        = Y     N  Y
pull_vec1       = 0.75 0  1
pull_start      = yes
pull_ngroups    = 1
pull_group0     = Chain_B
pull_group1     = Chain_A
pull_rate1      = 0.01
pull_k1         = 1000
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