[gmx-users] Pulling ion - US

Steven Neumann s.neumann08 at gmail.com
Mon Dec 10 15:01:25 CET 2012

Dear Gmx Users,

I am pulling away cation from the protein glutamic acid residue with:

pull            = umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim        = N N Y
pull_start      = yes       ; define initial COM distance > 0
pull_ngroups    = 1
pull_group0     = Protein
pull_group1     = NA
pull_rate1      = 0.01
pull_k1         = 500      ; kJ mol^-1 nm^-2

I tried different pulling rates and simulation time to pull it 3 nm
away. I tried pull rate of 0.1; 0.01 and 0.001. The interaction is so
strong that the force reaches 600 kJ/mol/nm2 and they do not become
separated - with position restraints protein looses its secondary
structure and is draged by the ion - they do not become separated.

Would you suggest constant force pulling in this case? Then I will
extract initial coordinates for US windows. Can I use then US with
harmonic potential in windows then and WHAM?


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