VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Sun May 06 2018 - 15:40:51 CDT

Given the nature of the problem, i don't think uninstalling and
reinstalling is going to fix it.
Given that different sized systems result in the freezeup/crash at
different stages (from loading to any later time) this could be because of
a outdated drivers amongst other things.

Perhaps try updating your drivers - if they are outdated.

On Mon, May 7, 2018 at 3:58 AM, Jacob F. Tande <fossotaj_at_gmail.com> wrote:

> Your computer has 8Gb of RAM but how much of that is free? If you know how
> much memory is available for use besides normal processes, then that can
> give you a great idea of what is happening.
>
> When you run VMD and load the file how much memory do you still have
> available.
>
> From what you are saying, it appears you are short on resources.
>
> The "top" command would be pretty helpful to you.
>
> Good luck
>
> On Sun, May 6, 2018, 9:35 AM locuswendy <locuswendy_at_gmail.com> wrote:
>
>> Dear Ashar:
>>
>> Thanks for your reply. I am answering you between lines,
>>
>> Does the trajectory load fully?
>>
>>
>> —> When it loads, yes
>>
>>
>> Does it show the number of frames have loaded?
>>
>>
>> —> When it loads, yes
>>
>>
>> If you try to do these operations while the structure is loading it will
>> not be responsive.
>>
>>
>> —> I try after the Protein Structure File is already charged. Even I can
>> try many many minutes later, sometimes it does not charge (the most of the
>> times).
>>
>> Is it just the visualisation state that gets frozen?
>>
>>
>> —> Not only
>>
>> Or does VMD crash?
>>
>>
>> —> Sometimes
>>
>> What RAM do you have on your computer and what are the sizes of the .dcd
>> files you are trying to load.
>>
>>
>> —> 8 GB RAM and the sizes are variable. As I said, the problem is
>> (between others) that many times when I tried the choice “Load Data Into
>> Molecule” even for a .pdb of 2MB it does not work. I tried yesterday many
>> many times to upload using this choice a file of 2 MB but onFriday I tried
>> a .dcd file of more than 850 MB and it worked after the third trial.
>>
>>
>> Try loading smaller trajectories? Can you reproduce the problem using a
>> smaller trajectory?
>>
>>
>> —> I tried many choices, the problem is reproducible the most of the
>> time, but sometimes VMD works…I am a VMD user for 14 years. This is the
>> first time I have this problem.
>>
>> Regards,
>>
>> Wendy
>>
>>
>>
>> El 06-05-2018, a las 1:45, Ashar Malik <asharjm_at_gmail.com> escribió:
>>
>> Does the trajectory load fully? Does it show the number of frames have
>> loaded? If you try to do these operations while the structure is loading it
>> will not be responsive.
>>
>> Is it just the visualisation state that gets frozen? Or does VMD crash?
>> What RAM do you have on your computer and what are the sizes of the .dcd
>> files you are trying to load.
>>
>> Try loading smaller trajectories? Can you reproduce the problem using a
>> smaller trajectory?
>>
>> On Sun, May 6, 2018 at 4:04 PM, locuswendy <locuswendy_at_gmail.com> wrote:
>>
>>> Dear VMD users:
>>>
>>> I am having big troubles to visualize properly using VMD 1.9.2 in my
>>> MacBook Pro. I am using Intel Graphics. It is really difficult to
>>> visualize, for example, a .dcd file or another that you most use the choice
>>> “Load Data Into Molecule”. Sometimes the visualization state get frozen and
>>> I can not rotate, translate, scale..anything. It is really a nightmare and
>>> although I´ve installed VMD many times (removed and installed again, many
>>> many times), the problems always come…Any help?
>>>
>>>
>>
>>
>> --
>> Best,
>> /A
>>
>>
>> 

-- 
Best,
/A