current Gromacs to do it.
-Jianguo
From: Netaly Khazanov
To: gmx-users@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 cal
On 10/17/12 9:17 AM, Netaly Khazanov wrote:
Thanks.
However, I can restrain the position of backbone (x,y,z -coordinates) while
running umbrella sampling and treat it like reaction coordinate. Is it
right?
Maybe I am missing something.
pull = umbrella
pull_geometry = position
;pull_dim = Y
Thanks.
However, I can restrain the position of backbone (x,y,z -coordinates) while
running umbrella sampling and treat it like reaction coordinate. Is it
right?
Maybe I am missing something.
pull = umbrella
pull_geometry = position
;pull_dim = Y Y Y
pull_start = yes
pull_ngroups = 1
;pull_grou
On 10/17/12 5:44 AM, Netaly Khazanov wrote:
Of course I read Justin's tutorial.
The reason I am asking is that I am not sure how to do it.
As far as I am aware, there is no way to conduct umbrella sampling in this way
using Gromacs. The PMF calculations that Gromacs does are based on restr
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 <
armansoufi...@gmail.com> wrote:
> Hi,
>
> I recommend you Justin's tutorial on Umbrella Sampling
>
> http://www.bevanlab.biochem.vt.edu/Pages/
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 wrote:
> Dear All,
>
> I've performed TMD simulation using NAMDprogram. I'd lik
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
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