[Chimera-users] Chimera Molecular Dynamics

[Benjamin Strickland]

I still believe something is weird with the calculation, this is only a
single molecule and I left it overnight and it still did not finish
updating, yet the actual minimization step in the beginning took approx. 30
seconds to compute.  I attached a screenshot of where the program appears
to hang up down below.

Regards,
Benjamin

On Wed, Jul 1, 2020 at 12:20 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> After it finishes actually computing the trajectory, there is a period of
> time where it only uses one CPU as it brings up the Movie dialog and
> finishes writing the trajectory files.  This period of time can actually be
> awhile if you computed many trajectory steps.
>
> --Eric
>
> On Jun 30, 2020, at 9:55 PM, Benjamin Strickland <bstrickland at drew.edu>
> wrote:
>
> I will give it another try, perhaps I set something up incorrectly? But
> when saving in "MMTK updating coordinates" for example definitely only one
> core is being utilized
>
> Regards,
> Benjamin
>
> On Tue, Jun 30, 2020, 6:11 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>
>> Sorry, I'm kind of stumped.  This does not happen for me.  When I run
>> solvated MD on 2gbp, it uses all of my cores (4) for all phases of the
>> computation.  Also, the trajectory updates continuously.  You should be
>> aware that the frame-to-frame motion is very slow and easy to miss --
>> though once bonds start crossing the periodic box it becomes more obvious
>> as the long cross-box bonds appear and disappear every half-dozen frames or
>> so.
>>
>> Not sure why things would behave differently on your machine.
>>
>> --Eric
>>
>> On Jun 29, 2020, at 11:05 AM, Benjamin Strickland <bstrickland at drew.edu>
>> wrote:
>>
>> Thank you for the quick response!
>>
>> I have 24 cores on the CPU and selected the multi CPU option.  Running
>> the initial minimization and heating of a ligand molecule took
>> approximately 20minutes and all cores were used after which the molecule
>> became a mess of lines which I read is normal and is representative of the
>> moved atoms?  However, after this point it appears the software is only
>> using one core on the CPU rather then all 24.
>>
>> Additionally despite checking live trajectory I do not see the image
>> updating only the final mess of lines image.
>>
>> Regards,
>> Benjamin
>>
>> On Mon, Jun 29, 2020, 12:13 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>>
>>> Hi Benjamin,
>>> MD calculation is a slow process, particularly for a large solvated
>>> system.  If you want visual feedback as the calculation progresses, check
>>> the "Live trajectory" box in the "other runtime options" setting under the
>>> "Run Parameters" tab.  To speed things (assuming you have multiple CPUs)
>>> you should also check the "Use multiple CPUs" box on that same page.
>>>
>>> --Eric
>>>
>>> Eric Pettersen
>>> UCSF Computer Graphics Lab
>>>
>>>
>>> On Jun 28, 2020, at 9:49 PM, Benjamin Strickland <bstrickland at drew.edu>
>>> wrote:
>>>
>>> Hello,
>>>
>>> I have recently started playing around with the MD tool in chimera,
>>> however I have noticed something odd.  I set up the simulation and begin
>>> running it however, upon completion of the initial minimization I reach the
>>> "MMTK updated coordinates" step and heating.nc files appear on the
>>> desktop.  However, after this point the application has a (not responding)
>>> and there appears no be very little usage of the CPU.  I am unsure if
>>> something is going wrong or I have to simply wait longer as I see no
>>> indication of any pending process or status.  I am running Windows 10 and
>>> the CPU is a AMD Threadripper 3960x.
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