[gmx-users] pulling experiment

[Justin A. Lemkul]

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 <jalemkul at vt.edu 
> <mailto:jalemkul at 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: zhangxh at fudan.edu.cn <mailto:zhangxh at fudan.edu.cn>
>         <mailto:zhangxh at fudan.edu.cn <mailto:zhangxh at fudan.edu.cn>>
>         Email: xhzhang2009 at sinano.ac.cn
>         <mailto:xhzhang2009 at sinano.ac.cn>
>         <mailto:xhzhang2009 at sinano.ac.cn <mailto:xhzhang2009 at 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: zhangxh at fudan.edu.cn <mailto:zhangxh at fudan.edu.cn>
> Email: xhzhang2009 at sinano.ac.cn <mailto:xhzhang2009 at 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

========================================