VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Oct 02 2019 - 15:07:54 CDT

madhur,

it seems, that you are not understanding periodic boundary conditions
properly.
with PBC, the choice of origin of your box is irrelevant and should not
(outside of some very minimal rounding issues due to using floating point
math) in any way impact your simulation results.
it is because of this translation invariance, that the total number of
degrees of freedom has to be reduced by 3 from 3N to 3N-3.

axel.

On Wed, Oct 2, 2019 at 2:24 PM Madhur Aggarwal <
madhur.aggarwal_at_research.iiit.ac.in> wrote:

> I am extremely sorry I didn't complete my question in my previous mail
> before hitting enter by mistake ..
>
> So, for visualization, I can use -center origin flag to see my system
> centred inside one simulation box, but in reality when I run my simulation,
> as half of my system is outside the box, the pbc conditions will wrap the
> atoms and the environment for those atoms would change. I do not want this
> to happen. I want my system should remain well inside one box during the
> entire simulation (I will also restrict the COM motion to make sure of
> that).
> Because I am specifying my simulation box to be centered at origin itself
> from the start (by specifying xlo, xhi as -10.0, 10.0 respectively, same
> for all 3 dimensions) and still it is not working, I am not sure how to
> achieve this.
>
> I am attaching a screenshot of my system with simulation box which I get
> after pbc box command, with and without using -center origin flag.
>
> Thanks again,
> Madhur Aggarwal
> ------------------------------
> *From:* Madhur Aggarwal <madhur.aggarwal_at_research.iiit.ac.in>
> *Sent:* Wednesday, October 2, 2019 11:21 PM
> *To:* Bassam Haddad <bhaddad_at_pdx.edu>; Giacomo Fiorin <
> giacomo.fiorin_at_gmail.com>
> *Cc:* vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
> *Subject:* Re: vmd-l: lammps data file simulation box center and VMD
> origin
>
> Hi Bassam, Giacomo
>
> Thanks a lot for your prompt reply. I could center my system at the origin
> now. With the use of "pbc box -center origin" command, I could also center
> my simulation box at the origin (same as my system). But I have a small
> doubt here: When I use just "pbc box" command, my simulation box is placed
> somewhere else (even when I am specifying in my lammps data file to center
> it on origin (0,0,0)). In this case, onl y a small portion of my system is
> inside the box and the rest is outside.
> So, for visualization, I can use -center origin flag to see my system
> centred inside one simulation box, but in reality when I run my simulation,
> as half of my system is outside the box, the pbc conditions will wrap the
> atoms and the environment for those atoms would change.
> ------------------------------
> *From:* Bassam Haddad <bhaddad_at_pdx.edu>
> *Sent:* Wednesday, October 2, 2019 9:48 PM
> *To:* Madhur Aggarwal <madhur.aggarwal_at_research.iiit.ac.in>
> *Cc:* vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
> *Subject:* Re: vmd-l: lammps data file simulation box center and VMD
> origin
>
> Hi Madhur,
>
> # select atoms in your system
> set all [atomselect top all]
>
> # find the geometric center of the atoms
> measure center $all
> > x y z (assume these values are not 0)
>
> # move your system to the center (0,0,0)
> $all moveby {-x -y -z}
>
> That should do it.
>
> Bassam
>
>
> On Wed, Oct 2, 2019 at 8:55 AM Madhur Aggarwal <
> madhur.aggarwal_at_research.iiit.ac.in> wrote:
>
> Hi all,
>
> I am beginner in VMD. I have a lammps data file which contains the
> dimensions of my simulation box. I want to translate my system to the
> center of the box. It would be great if someone could help me in figuring
> out how to do it.
> Also, in my lammps data file, my simulation box dimensions are:
>
> -10.000 10.000 xlo xhi
> -10.000 10.000 ylo yhi
> -10.000 10.000 zlo zhi
>
> So VMD origin should be at the center of my simulation box, which is not
> the case when I visualize it by using "pbc box" command. I am not sure why
> this is happening.
>
> Thanks in advance,
> Madhur Aggarwal
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.