VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jun 25 2015 - 10:45:51 CDT

On Thu, Jun 25, 2015 at 11:39 AM, Vidyalakshmi CM
<vidyalakshmi.cm_at_gmail.com> wrote:
> Dear Sir,
>
> The gromacs analysis/check programs were performed on the same computer
> platform (like linux).

but if i understand your (rather vague and incomplete) description
correctly, you get the problems reading the trajectory on a different,
a windows machine.
so that does not exclude the possibility that your files got corrupted
during data transfer or that you have a defective file system or
defective hardware or reaching some file system limit.

> The version of VMD I am using is VMD 1.9.1.
>
> Is there a way to check if VMD is reading the file correctly.

how large is this file?

you can try reading reading the file on the same machine where you ran
the simulation. just install VMD yourself and run it in text mode and
manually load the file in text mode. please note that VMD 1.9.2 has a
bug in the gromacs molfile plugin, and you need to update the plugins
with corrected versions.

axel.

>
> Thanks and Best Regards,
> C.M.Vidyalakshmi
>
> On Thu, Jun 25, 2015 at 4:29 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> 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.
>
> 

-- 
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.