[gmx-users] Umbrella sampling after TMD of NAMD

[Arman Mahboubi Soufiani]

Hi,

I recommend you Justin's tutorial on Umbrella Sampling
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html

Regards

Arman

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
> GROMACS.
> 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
> --
> Netaly
> --
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