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: [email protected] <[email protected]> en nombre de Justin Lemkul <[email protected]> Enviado: miércoles, 15 de febrero de 2017 08:02 a. m. Para: [email protected] 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 -- ================================================== 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 [http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]<http://mackerell.umaryland.edu/~jalemkul> Welcome to my site! - University of Maryland, Baltimore<http://mackerell.umaryland.edu/~jalemkul> mackerell.umaryland.edu Welcome to my site! To learn more about me and the work I am doing, please use the navigation links above. ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! GMX-Users List - Gromacs<http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> www.gromacs.org This is the main discussion forum for users of GROMACS and related software. Subscribe, unsubscribe or change your preferences through gmx-users Admin page. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Mailing Lists - Gromacs<http://www.gromacs.org/Support/Mailing_Lists> www.gromacs.org The three mailing lists (see the menu items on the left) have slightly different purposes, and you might not be interested in subscribing to all of them: * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected]. gromacs.org_gmx-users Info Page - Royal Institute of ...<https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> maillist.sys.kth.se gromacs.org_gmx-users -- Discussion list for GROMACS users About gromacs.org_gmx-users -- 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].
