[gmx-users] Center of mass: distance restrain for groups
Hualin.Li at uth.tmc.edu
Fri Oct 7 20:22:46 CEST 2011
Dear GMX users,
I am using pull code to make a distance restrain to my proteins and membrane,which looks like this:
pull = umbrella
pull_geometry = cylinder
pull_vec1 = 0 0 1
pull_r1 = 2.5
pull_r0 = 2.5
pull_dim = N N Y ;# 3D
pull_start = yes ;# add COM distance to initial value (initial value = equilibrium value)
pull_ngroups = 32 ;# excluding the reference
pull_group0 = membrane ;# the reference group - the membrane
pull_pbcatom0 = -1 ;# or -1 - important for PBC of groups larger than half box,
;# as here for membrane (see manual)
pull_group1 = protein ;# the protein
pull_pbcatom1 = 0 ;# here is no issue since protein is smaller than half the box
pull_rate1 = 0 ;# do not pull, just maintain distance!
pull_k1 = 800 ;# kJ mol^(-1) nm^(-2)
However, I have 32 protein to keep this local dynamic distance restrain ( pull_geometry = cylinder ), making the calculation goes very slowly. Is there any method to reduce the frequency to update the dynamic distance check and restrain please?
Thank you in advance.
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