[gmx-users] Umbrella sampling after TMD of NAMD

[Netaly Khazanov]

Of course I read Justin's tutorial.
The reason I am asking is that I am not sure how to do it.

On Wed, Oct 17, 2012 at 11:09 AM, Arman Mahboubi Soufiani <
armansoufiani at gmail.com> wrote:

> 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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-- 
Netaly