VMD-L Mailing List

From: Sandip Mondal (sandchem13_at_gmail.com)
Date: Mon Mar 26 2018 - 01:26:23 CDT

Dear Christian,

  Thank you very much for your detail description.

Thanking you,
Sandip

On Sat, Mar 24, 2018 at 11:26 AM, Christian Leitold <
christian.leitold_at_gmail.com> wrote:

> 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.
>>>>>
>>>>
>>>>
>>>
>>
>