VMD-L Mailing List

From: Sandip Mondal (sandchem13_at_gmail.com)
Date: Sat Mar 24 2018 - 00:04:49 CDT

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.
>>>
>>
>>
>