[gmx-users] gmx dipoles with dynamic indices (gromacs 5.0.x)

[Daskalakis Vangelis]

Thank you Justin,
Yes, that would do the work. I thought there could be another way, but I
won't avoid doing it frame by frame.
Thank you again.

On Wed, Sep 16, 2015 at 2:55 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/15/15 6:13 PM, Daskalakis Vangelis wrote:
>
>> Hello.
>> I want to use a dynamic selection scheme (select different atoms based on
>> the same selection criteria for each frame of a trajectory) and pass this
>> selection/ info to the gmx dipoles tool. It seems that the -select option
>> cannot be used.
>> I tried to use dynamic selection through gmx select. The gmx select output
>> (using the -on option, e.g an index.ndx file) was indeed a correct
>> selection of the molecules/ atoms within the system for each frame,
>> resulting in a large index.ndx file for the whole trajectory.
>> When I use the -n index.ndx option for the gmx dipoles, there is of course
>> this huge list of groups of atoms (one group per frame) showing up. I
>> cannot choose just one frame selection group, as I want the gmx dipoles
>> tool to process each frame based on the selected group of atoms for each
>> frame written in index.ndx by gmx select.
>> Any ideas or suggestions? Thank you.
>>
>>
> You'll have to do the analysis frame by frame in a shell script.  Use the
> index group as a counter, and then calculate what the time is based on the
> interval you've saved and pass that value to gmx dipoles -b -e.  See also
>
> http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
>
> So your first call (for the first frame, t=0) is:
>
> echo 0 | gmx dipoles -b 0 -e 0 -s *.tpr -f *.xtc/trr
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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