[gmx-users] Accelerating data analysis.

[Dawid das]

Dear Krzysztof,

do you convert *trr to *xtc after your simulation or do you write data to
the latter one as it proceeds?

Dawid

2015-09-15 15:57 GMT+01:00 Krzysztof Kuczera <kkuczera at ku.edu>:

> Since most of my analyses deal with the protein part, I typically use
> trjconv to make an .xtc trajectory with protein coordinates only. Running
> most analyses on that file is at least 10x faster than on whole .trr
> Krzysztof
>
> On 9/15/15 7:42 AM, Erik Marklund wrote:
>
>> 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
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>
>
> --
> Krzysztof Kuczera
> Departments of Chemistry and Molecular Biosciences
> The University of Kansas
> 1251 Wescoe Hall Drive, 5090 Malott Hall
> Lawrence, KS 66045
> Tel: 785-864-5060 Fax: 785-864-5396 email: kkuczera at ku.edu
> http://oolung.chem.ku.edu/~kuczera/home.html
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>