From: Christian Leitold (christian.leitold_at_gmail.com)
Date: Fri Mar 23 2018 - 14:17:58 CDT

Hi Sandip,

You can certainly move molecules around in VMD, and Josh's answer should
give you some hints.

However, am I right in assuming that actually you want to run a
_simulation_ where the relative distance between the two molecules is
varied? VMD does not do simulation, just visualization...

Best,
Christian

On 23 March 2018 at 10:42, Sandip Mondal <sandchem13_at_gmail.com> wrote:

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.
>>
>
>