From: Jacob F. Tande (fossotaj_at_gmail.com)
Date: Sun May 06 2018 - 10:58:19 CDT

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
>
>
>