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 Y Y
pull_start = yes
pull_ngroups = 1
;pull_group0 =0
pull_group1 = backbone
pull_init1 = 0
pull_rate1 = 0.0
With this approach, you restrain the backbone with respect to no specific group
(i.e. an absolute restraint), so the PMF is based on the position of the
backbone of the protein, not the value of its RMSD.
-Justin
On Wed, Oct 17, 2012 at 2:37 PM, Justin Lemkul <jalem...@vt.edu> wrote:
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
restrained distances or angles. I do not believe one can set an arbitrary
variable like RMSD to be a reaction coordinate in the same sense, and
certainly the pull code is not applicable in this instance.
-Justin
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/Personal/justin/**
gmx-tutorials/umbrella/index.**html<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 <neta...@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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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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