[gmx-users] Accelerating data analysis.

[Erik Marklund]

Well not necessarily, but it depends on how badly you want to avoid it. Your command line with g_rms -tu us -b ... seemed correct, and it seems to be skipping frames just like you instructed it to.

Erik

> On 15 Sep 2015, at 14:35, Dawid das <addiw7 at googlemail.com> wrote:
> 
> Thank you again. So after all I still need trjconv.
> 
> 
> 2015-09-15 14:24 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:
> 
>> Hi,
>> 
>> Yes. There is no intelligence about .trr reading (unlike .xtc) so it reads
>> every frame until one that satisfies your constraint. You will have a
>> better time implementing Erik's strategy if you break the trajectory into
>> parts with trjconv, convert it to .xtc, or write it as .xtc in the first
>> place. See also
>> 
>> http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume
>> 
>> Mark
>> 
>> On Tue, Sep 15, 2015 at 2:59 PM Dawid das <addiw7 at googlemail.com> wrote:
>> 
>>> 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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