[gmx-developers] reading non-gromacs trajectory formats and adding of default extension

[Roland Schulz]

Hi Chris,

thanks for the question.

This made me realize that I changed the default behavoir more than makes
sense at this moment.

I don't think it is a good idea to not append the default filetype to output
files. And even for input files it is in general not good. Because the
filetype is based on the ending. And for non-trajectory input it has to be
one of the GROMACS types.

So I reverted the default behavior unless for reading of trajectory data.
Because there it makes sense and also has no weird side effects.

For your problem:
There is a noconfout option to mdrun. May be we should add also a -nolog
option and don't create the trajectory or energy file if anything is written
(if nstenergy/nstxout is 0).

Roland

On Thu, Nov 26, 2009 at 9:07 AM, <chris.neale at utoronto.ca> wrote:

> Hi Roland,
>
> You mention that now "The default extension is only added if the specified
> file does not exist." Does this mean that I can now do this:
>
> mdrun -deffnm this -o /dev/null -c /dev/null -g /dev/null
>
> This would be very convenient to alleviate demand on our file system where
> we are running very many very short simulations and the opening/closing is
> beginning to cause problems.
>
> Thanks,
> Chris.
>
>
> Quoting Roland Schulz <roland at utk.edu>:
>
>  Hi,
>>
>> I just commited the Gromacs support for the VMD molfile plugin API.
>>
>> This allows all analysis tools to read all VMD supported trajectory
>> formats
>> (e.g. DCD).
>> It requires a VMD binary compiled with the same architecture as GROMACS
>> (e.g. both 64bit).
>> It is by default compiled in in case dlopen is supported (thus for all
>> mayor
>> architectures).
>>
>> It changes one earlier behavior (even if dlopen support is not compiled
>> in):
>> The default extension is only added if the specified file does not exist.
>> e.g. if both the file file.dcd and test.dcd.xtc exist then g_rms -f
>> test.dcd
>> reads file.dcd and not test.dcd.xtc.
>>
>> Roland
>>
>> --
>> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
>> 865-241-1537, ORNL PO BOX 2008 MS6309
>>
>>
>
>
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-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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