VMD-L Mailing List

From: Christian Leitold (christian.leitold_at_gmail.com)
Date: Sat Mar 24 2018 - 00:56:46 CDT

Sandip,

You said you already have the center-of-mass coordinates of A and B. Good,
that's a start. Now, shift everything so that A's center of mass is at the
origin (0, 0, 0), i. e. you just subtract the com coordinates from each
point. Next, get the vector from A to B. transvecinv will give you the
rotation matrix to rotate the vector to the x axis. Apply this
transformation to your system, and you are done.

Best,
Christian

On 23 March 2018 at 22:04, Sandip Mondal <sandchem13_at_gmail.com> wrote:

> Hello Christian,
>
> Thanks for your reply.
>
> Your assumption is partially correct. From VMD I will generate the
> initial structure.
> I'll not perform simulation using VMD.
>
> However till now I can't apply Josh's hint to my system.
>
> Thanking you,
> Sandip
>
>
> On Sat, Mar 24, 2018 at 12:47 AM, Christian Leitold <
> christian.leitold_at_gmail.com> wrote:
>
>> 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.
>>>>
>>>
>>>
>>
>