[gmx-users] Error select a group gmx_density

[Poncho Arvayo Zatarain]

Ok, thanks Justin. But i have one more question: What do you mean with syntax make_ndx? Is the way the command is writting: gmx_gpu density -ng 4 -f npt06.xtc -s npt06.tpr -o density.xvg? Is there anoher way to wrtie the command for density?

________________________________
De: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> en nombre de Justin Lemkul <jalemkul at vt.edu>
Enviado: miércoles, 15 de febrero de 2017 08:02 a. m.
Para: gmx-users at gromacs.org
Asunto: Re: [gmx-users] Error select a group gmx_density



On 2/15/17 10:55 AM, Poncho Arvayo Zatarain wrote:
>
> Hello Gromacs users: I´m trying to obtain the density og a mixed membrane
> plus a protein. I use the command line:  gmx_gpu density -ng 4 -f npt.xtc -s
> npt.tpr -o density.xvg. And this appears: Reading file npt.tpr, VERSION 5.0.4
> (single precision)
>
> Select 4 groups to calculate density for: Group     0 (         System) has
> 58780 elements Group     1 (          Other) has 58780 elements Group     2 (
> PROTEIN) has   576 elements Group     3 (           DPPC) has 16640 elements
> Group     4 (           DPPE) has 15488 elements Group     5 (
> TIP3) has 26076 elements Select a group: 3 & 4 & 2 & 5 Selected 3: 'DPPC'
> Select a group: Error: No such group '&' Select a group: Selected 4: 'DPPE'
> Select a group: Error: No such group '&' Select a group: Selected 2:
> 'PROTEIN' Select a group: Error: No such group '&' Select a group: Selected
> 5: 'TIP3' Last frame       5000 time 210000.000
>
> Read 5001 frames from trajectory. Calculating density
>
> Is there anything wrong with the command line or with Select a group: Error:
> No such group '&'? Also i tried with 3 | 4 | | 2 | 5 and appears the same
> error but with | instead &? What about the Last frame 5000 time 210000.000?

You can't use make_ndx style syntax with gmx density.  You should be prompted
for 4 selections, individually.  Otherwise, just calculate the density of each
group separately.

> Why 5000 and not 210000.000?. Also, and .xvg file is generated Thanks
>

What should the time be?  What is printed to the terminal is just a running
indicator of progress; it is not a definitive statement of the contents of the
trajectory.  For that, use gmx check (or look in the .xvg file to see the time
values).

-Justin

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