[gmx-users] Umbrella sampling after TMD of NAMD
Arman Mahboubi Soufiani
armansoufiani at gmail.com
Wed Oct 17 11:09:30 CEST 2012
I recommend you Justin's tutorial on Umbrella Sampling
On Wed, Oct 17, 2012 at 10:47 AM, Netaly Khazanov <netalyk at gmail.com> wrote:
> 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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