[gmx-users] pulling experiment

[Xiaohua Zhang]

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.

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?

cheers
xiaohua

On Mon, Sep 20, 2010 at 10:04 AM, Justin A. Lemkul <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>
>> 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
>
> ========================================
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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
Email: xhzhang2009 at sinano.ac.cn
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