VMD-L Mailing List

From: Sandip Mondal (sandchem13_at_gmail.com)
Date: Fri Mar 23 2018 - 12:42:45 CDT

Dear Axel,

    Sorry, it was my mistake.

    Thanks for your response.

    Let say, I have a complex system form between two molecule "A" and "B".
So from the atomic coordinate I can calculate center of mass of individual
molecule "A" and "B". Now the connector between those two points will give
a straight line. My requirement is that I want to see that line as parallel
to an
axis (e.g Z axis). So for that I need to rotate the complex in such way that
the connecting line becomes parallel to Z axis. I want to know that how it
can
be done by vmd.
     Actually I want to move one part of that molecule along that axis by
keeping
fixed the other one.

     I will use CUDA for simulation purpose.

Thanking you,
Sandip

On Fri, Mar 23, 2018 at 10:59 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> please always reply to the mailing list and not only individual
> people. thanks, axel.
>
> On Fri, Mar 23, 2018 at 1:21 PM, Sandip Mondal <sandchem13_at_gmail.com>
> wrote:
> > Dear Axel,
> >
> > Thanks for your response.
> >
> > Let say, I have a complex system form between two molecule "A" and
> "B".
> > So from the atomic coordinate I can calculate center of mass of
> individual
> > molecule "A" and "B". Now the connector between those two points will
> give
> > a straight line. My requirement is that I want to see that line as
> parallel
> > to an
> > axis (e.g Z axis). So for that I need to rotate the complex in such way
> that
> > the connecting line becomes parallel to Z axis. I want to know that how
> it
> > can
> > be done by vmd.
> > Actually I want to move one part of that molecule along that axis by
> > keeping
> > fixed the other one.
> >
> > I will use CUDA for simulation purpose.
> >
> >
> > Thanking you,
> > Sandip
> >
> >
> >
> > On Fri, Mar 23, 2018 at 8:27 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> >>
> >> On Fri, Mar 23, 2018 at 10:31 AM, Sandip Mondal <sandchem13_at_gmail.com>
> >> wrote:
> >> > Dear user,
> >> >
> >> > How to parallelize a line, form between two center of mass of two
> >> > molecules to an axis (let say Z axis) in vmd?
> >>
> >> i know how to parallelize a computation, but i am curious about how to
> >> "parallelize a line". can you please explain in more detail?
> >> would you use MPI or OpenMP or CUDA or something else?
> >>
> >> thanks,
> >> axel.
> >>
> >> >
> >> > Thanking you,
> >> > Sandip
> >> >
> >>
> >>
> >>
> >> --
> >> 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.
> >
> >
>
>
>
> --
> 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.
>