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 [email protected] | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
