VMD-L Mailing List

From: Tim Lo (timlo_at_connect.hku.hk)
Date: Fri Jul 10 2015 - 22:08:19 CDT

Hi Richard,

When you load large dcd files, it's better to choose "Load all at once"
option. It allows you to load slightly more frames into VMD. "Load all
at once" uses less memory during loading than "Load in background".

Tim
Research Associate
The University of Hong Kong

On 7/7/2015 9:56, Richard Wood wrote:
> What you suggested worked, Axel. I was able to read the dcd from frame 300 to the end and (frame 336) and I saved the coordinates from frame 336.
>
> The file is rather large (it's a ~1000 per leaf POPC bilayer with waters, of course). Take that @ 337000 steps and you've got a large file. I have 4 GB of RAM in a Win 7 box. To be honest, there is no "error message" when it crashes-I just get the standard "Program is not responding" message, and then it closes.
>
> Richard
> ________________________________________
> From: Axel Kohlmeyer [akohlmey_at_gmail.com]
> Sent: Monday, July 06, 2015 8:45 PM
> To: Richard Wood
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: reading in trajectory file causes VMD to crash
>
> On Mon, Jul 6, 2015 at 9:14 PM, Richard Wood
> <Richard.Wood_at_purduecal.edu> wrote:
>> Well, I don't know what you call it when the file causes the program to crash other than "too large to read"-over loads memory maybe?
> as i said, it shouldn't consume much memory, if you skip most frames
> on loading. VMD only allocates memory for data that you tell it to
> keep.
>
> how large is the file, how much RAM does you machine have and what OS
> are you running on?
> do you get some info/error on the command window before it crashes?
>
> axel.
>
>> Richard
>> ________________________________________
>> From: Axel Kohlmeyer [akohlmey_at_gmail.com]
>> Sent: Monday, July 06, 2015 8:12 PM
>> To: Richard Wood
>> Cc: vmd-l_at_ks.uiuc.edu
>> Subject: Re: vmd-l: reading in trajectory file causes VMD to crash
>>
>> On Mon, Jul 6, 2015 at 8:52 PM, Richard Wood
>> <Richard.Wood_at_purduecal.edu> wrote:
>>> Hi all,
>>>
>>> I have a simulation that has run for 337000 steps, but, unfortunately, has crashed. 337 steps have been written to a dcd file. The resultant dcd file is too large to read into VMD (the program crashes after reading in about 250 frames or so). Is there any workaround for me to get the last structure so I can start my simulation again? All I have is the starting geometry, the psf and the dcd file (no other restart files). Surely there is something I can read this file into.
>> i don't get the "too large to read" part. if all you care about is the
>> last few frames, just tell VMD to skip over the first 300 or so by
>> changing the entry of the first frame to load in the file load dialog.
>>
>> axel.
>>
>>> TIA,
>>> Richard
>>>
>>
>>
>> --
>> 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.
>