Basic question: How do I verify that the right atoms were chosen in the index file? There are a lot of atoms.
On Wed, Sep 25, 2013 at 9:52 PM, rajat desikan <rajatdesi...@gmail.com>wrote: > Thank you very much. My bilayers were initially built with packmol which > is probably why z>6 worked. I will keep this in mind. > > > On Wed, Sep 25, 2013 at 9:46 PM, Teemu Murtola <teemu.murt...@gmail.com>wrote: > >> Hello, >> >> On Wed, Sep 25, 2013 at 5:48 PM, rajat desikan <rajatdesi...@gmail.com >> >wrote: >> >> > I have a dopc+50% cholesterol bilayer. I want to selectively choose the >> > upper and lower leaflets. I used g_select the following way >> > g_select -s DOPC_0.5chl.gro -select 'resname DOPC and resname >> Cholesterol >> > and z>6' (6 is the COM of my box) >> > >> > I am getting the following error. >> > Possible bug: >> > one of the values for comparison missing >> > >> > g_select -s DOPC_0.5chl.gro -select 'resname DOPC and resname >> Cholesterol' >> > works perfectly fine. What is the problem? >> > >> >> Your problem is that 'resname DOPC and resname Cholesterol' by definition >> selects zero atoms. Try 'resname DOPC Cholesterol' instead. I will fix the >> error message, but most likely not in any upcoming 4.6.x releases. >> >> You may also find that unless you bilayer is very flat and static, you >> don't get exactly the atoms you want. Try 'resname DOPC Cholesterol and >> res_com z > 6'. >> >> Best regards, >> Teemu >> -- >> 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 >> > > > > -- > Rajat Desikan (Ph.D Scholar) > Prof. K. Ganapathy Ayappa's Lab (no 13), > Dept. of Chemical Engineering, > Indian Institute of Science, Bangalore > -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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
