VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jun 25 2015 - 10:29:11 CDT

On Thu, Jun 25, 2015 at 10:37 AM, Vidyalakshmi CM
<vidyalakshmi.cm_at_gmail.com> wrote:
> Dear Sir,
>
> I am using gromacs module 4.6.5 on a computing platform for parallel
> programming. I am working on this platform for the first time. And I am
> finding the same problem in more than one trajectory output files obtained
> from this system.
>
> I tried to download the file to my local machine (using Winscp) once at
> around 10 ns simulation (~2000 frames) and then I deleted this file in the
> local machine and downloaded again after completion of the simulation. (Such
> transfer of files on other computing platforms never resulted in files
> getting corrupted).
>
> The total number of entries in the log file is correct. And also when I am
> using gromacs programs that read .xtc trajectory (like for rmsd
> calculation), the number of timesteps read are correct ( i.e complete 24195
> ps)

did you run those gromacs analysis/check programs on windows?
otherwise it is not a convincing argument.

which version of VMD are you using?

> So, it looks like the number of files in the output trajectory are correct
> but they are not appearing in VMD.

unless you can provide me with a convincing proof that VMD is failing
on correct files, there is little that can be done.

axel.

> Please advise.
>
> Thanks and Best Regards,
> C.M.Vidyalakshmi
>
>
> On Thu, Jun 25, 2015 at 2:56 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> On Thu, Jun 25, 2015 at 9:29 AM, Vidyalakshmi CM
>> <vidyalakshmi.cm_at_gmail.com> wrote:
>> > Dear All,
>> >
>> > I am trying to visualize the gromacs output .xtc trajectory on VMD. I am
>> > generating .xtc trajectory frames every 5 ps. The total simulation run
>> > time
>> > is 24195 ps which should give me 4839 frames (without any skip).
>> > However,
>> > when I load frames say 4000 to 4100, I get the error message 'Error
>> > reading
>> > timestep, file does not match format'.
>> >
>> > With a skip of 10, I find the trajectory loads only initial frames (~200
>> > frames out of more than 480 which is expected). Please advise.
>>
>> this sounds like your trajectory file has been corrupted somehow.
>>
>> axel.
>>
>> >
>> > I have used VMD for viewing .xtc trajectories previously and have never
>> > had
>> > this issue previously.
>> >
>> > Please help.
>> >
>> > Thanks and Best Regards,
>> > C.M.Vidyalakshmi
>>
>>
>>
>> --
>> 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.