[gmx-users] Accelerating data analysis.

[Dawid das]

Something is wrong here. I use following command:

g_rms -tu us -b 0.9 -e 1.0 -s npt-md2.tpr -f npt-md2.trr -n index.ndx -o
rmsd-protein.xvg

and g_rmsd still starts from 0 and it says "Skipping frame..." and it seems
it will skip all frames (as it would read it) until 0.9 us.
Is that what I should expect?


2015-09-15 13:45 GMT+01:00 Dawid das <addiw7 at googlemail.com>:

> Dear All,
>
> Thank you all. Especially for your tip Erik ;).
>
> Dawid
>
> 2015-09-15 13:42 GMT+01:00 Erik Marklund <erik.marklund at chem.ox.ac.uk>:
>
>> Dear Dawid,
>>
>> The best thing I can think of is to analyse different parts of the
>> trajectory in parallel, using separate g_rms processes, then concatenating
>> the output. Use -b and -e options to limit the analysis to specific
>> intervals.
>>
>> Kind regards,
>> Erik
>>
>> > On 15 Sep 2015, at 13:37, Dawid das <addiw7 at googlemail.com> wrote:
>> >
>> > Dear Gromacs Experts,
>> >
>> > I have an enormous *trr file, which has 1 000 000 points. Now, I know
>> that
>> > I can modify this file with trjconv, but let's say I do not want to do
>> it,
>> > but I want to have my 1 000 000 points in *xvg file when I use g_rms for
>> > instance.
>> > Is there a way to accelarate it?
>> >
>> > Best wishes,
>> >
>> > Dawid Grabarek
>> > --
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