[gmx-users] Error select a group gmx_density

[Justin Lemkul]

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

-- 
==================================================

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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