[gmx-users] Umbrella sampling after TMD of NAMD

Netaly Khazanov netalyk at gmail.com
Wed Oct 17 10:47:45 CEST 2012

Dear All,

I've performed TMD simulation using NAMDprogram. I'd like to calculate PMF
plot based on the frames that were taken from TMD simulations by using
The  coordinate  of reaction is RMSD of backbone.
The first step is to do Umbrella sampling. The question is how fix the
position of backbone during the Umbrella sampling?
Is this looks reasonable?

pull            = umbrella
pull_geometry   = position
;pull_dim        = Y Y Y
pull_start      = yes
pull_ngroups    = 1
;pull_group0     =0
pull_group1     = backbone
pull_init1      = 0
pull_rate1      = 0.0
pull_k1         = 1000      ; kJ mol^-1 nm^-2
pull_nstxout    = 1000      ; every 2 ps
pull_nstfout    = 1000      ; every 2 ps

Any ideas how to convert the reaction coordinate from position of backbone
to RMSD of backbone in PMF plot?

Thank you in advance.

Netaly Khazanov

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