[gmx-users] Umbrella sampling after TMD of NAMD

Jianguo Li ljggmx at yahoo.com.sg
Wed Oct 17 16:13:28 CEST 2012

It seems difficult to use RMSD as the reaction coordinate to do umbrella sampling simulations. Maybe you can try meta-dynamics in which you can 
use RMSD as a collective to get the free energy. It is implemented in a 
modified version of gromacs (GROMETA), or you can use PLUMED together 
with current Gromacs to do it.

From: Netaly Khazanov <netalyk at gmail.com>
To: gmx-users at gromacs.org 
Sent: Wednesday, 17 October 2012, 16:47
Subject: [gmx-users] Umbrella sampling after TMD of NAMD

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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