[gmx-users] Error select a group gmx_density

Poncho Arvayo Zatarain poncho_8629 at hotmail.com
Wed Feb 15 17:18:40 CET 2017

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



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

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