Xiaohua Zhang wrote:
Sorry for my mistake about the group names.
I was confused just to find it difficult to simultaneously fix one group
(layer0) but pull another (layer2). It is possible to fix an absolute
reference and pull layer2, but layer0 might follow the motion of layer2.
For such experiment, the relative speeds between different layers are
the most important.
In my own MD code which can deal with only few kinds of atoms, I use a
constraint to fix the COM of layer0, and add a constant force on each
atom of layer2. My own MD can also do such thing, fix layer0 and slide
layer2 at constant velocity. It seems GROMACS can do the same thing, the
constant-speed sliding. However, I hope both can be done.
Both constant-velocity and constant-force pulling are possible.
Because I am a new user of GROMACS, I am thinking such a way:
Pulling layer2 by a constant force. (by using COM pulling parameters)
and
Fix layer0 by kinda constraint defined in the topology
does this work?
In Gromacs, "constraints" and "restraints" are different concepts. In order to
fix a group, you must apply either a position restraint or freeze the group.
Position restraints (I think) are more user-friendly and can be combined with
pressure coupling if an NPT ensemble is desired.
http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints
-Justin
cheers
xiaohua
On Mon, Sep 20, 2010 at 10:04 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Xiaohua Zhang wrote:
Dear gmx-users
I want to design such kind of computer experiment:
For a system composed of non-bonded three layers (carbon
nanotubes, graphene, or whatever), I want to fix layer0 (the
group name) to exactly (0,0,0), and pull layer2 by a constant
force, for example, along positive x all the time. The layer1 is
free to move. I am confused to define the COM pulling
parameters, under the latest GROMACS 4.5.1, because it seems
possible to pull layer2
pull = constant_force
pull_geometry = direction_periodic
pull_ngroups = 2
pull_group2 = layer2
pull_vec2 = 1.0 0.0 0.0
pull_k2 = a number in unit kJ mol-1 nm-1
but how about group1 ?
Could you give me some suggestion?
If group1 is free to move, i.e., not under the influence of any
pulling force, then it does not need to be considered in the pulling
section. So you will have one reference group (group0), one pull
group (pull_ngroup = 1), and all other groups pertain to group2
(which are then listed as pull_group1, pull_vec1, etc).
I don't know if you can simultaneously fix layer0 to (0,0,0) in this
scheme, since Gromacs builds all boxes relative to the origin (i.e.,
the box corner originates from the origin). If you leave
pull_group0 blank, then pulling on pull_group1 will be done with
respect to an absolute reference of (0,0,0).
http://manual.gromacs.org/current/online/mdp_opt.html#pull
-Justin
-Justin
cheers
xiaohua
--
Xiaohua Zhang
Suzhou Institute of Nano-Tech and Nano-Bionics
Ruoshui Road 398, Suzhou 215123, China
Phone: +86 512 62872552
Mobile: +86 137 71904040
Email: zhan...@fudan.edu.cn <mailto:zhan...@fudan.edu.cn>
<mailto:zhan...@fudan.edu.cn <mailto:zhan...@fudan.edu.cn>>
Email: xhzhang2...@sinano.ac.cn
<mailto:xhzhang2...@sinano.ac.cn>
<mailto:xhzhang2...@sinano.ac.cn <mailto:xhzhang2...@sinano.ac.cn>>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
Xiaohua Zhang
Suzhou Institute of Nano-Tech and Nano-Bionics
Ruoshui Road 398, Suzhou 215123, China
Phone: +86 512 62872552
Mobile: +86 137 71904040
Email: zhan...@fudan.edu.cn <mailto:zhan...@fudan.edu.cn>
Email: xhzhang2...@sinano.ac.cn <mailto:xhzhang2...@sinano.ac.cn>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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