[gmx-users] Error select a group gmx_density
jalemkul at vt.edu
Wed Feb 15 17:02:30 CET 2017
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
> 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
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
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