Re: [gmx-users] problem with volume equilibration
On 31/01/2012 5:14 PM, Anushree Tripathi wrote: When I run the command (i.e., grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr)for volume equilibration. I am getting the error: Fatal error: Group DPPC not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. Please guide me. Exactly like it says, you are using a group (DPPC) in your .mdp file that is not defined in the default groups. Either define it or stop using it. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem with volume equilibration
You'd better first your .top file, to see if you have included DPPC .itp file and also in the compound section. if it was ok, check the .ndx and look for the atom numbers of DPPC, after finding the atom numbers, make a group ( Like othe parts of .ndx; water, or protein,...) and name it DPPC. save and continue. Hope it help Sogol From: Anushree Tripathi anushritripa...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, January 31, 2012 9:44 AM Subject: [gmx-users] problem with volume equilibration When I run the command (i.e., grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr)for volume equilibration. I am getting the error: Fatal error: Group DPPC not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. Please guide me. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem with volume equilibration
How could I define the group for DPPC ? On Tue, Jan 31, 2012 at 11:57 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 31/01/2012 5:14 PM, Anushree Tripathi wrote: When I run the command (i.e., grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr)for volume equilibration. I am getting the error: Fatal error: Group DPPC not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. Please guide me. Exactly like it says, you are using a group (DPPC) in your .mdp file that is not defined in the default groups. Either define it or stop using it. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
