[gmx-users] g_select help
Hi All, 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 z6' (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? Thank you. -- 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 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] g_select help
Hello, On Wed, Sep 25, 2013 at 5:48 PM, rajat desikan rajatdesi...@gmail.comwrote: 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 z6' (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 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] g_select help
Thank you very much. My bilayers were initially built with packmol which is probably why z6 worked. I will keep this in mind. On Wed, Sep 25, 2013 at 9:46 PM, Teemu Murtola teemu.murt...@gmail.comwrote: 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 z6' (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 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 -- 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 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] g_select help
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.comwrote: Thank you very much. My bilayers were initially built with packmol which is probably why z6 worked. I will keep this in mind. On Wed, Sep 25, 2013 at 9:46 PM, Teemu Murtola teemu.murt...@gmail.comwrote: 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 z6' (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 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 -- 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 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] g_select help
On 9/25/13 12:24 PM, rajat desikan wrote: Basic question: How do I verify that the right atoms were chosen in the index file? There are a lot of atoms. Pass the index file to trjconv and use it to parse out the atoms in the group from the original coordinate file. -Justin On Wed, Sep 25, 2013 at 9:52 PM, rajat desikan rajatdesi...@gmail.comwrote: Thank you very much. My bilayers were initially built with packmol which is probably why z6 worked. I will keep this in mind. On Wed, Sep 25, 2013 at 9:46 PM, Teemu Murtola teemu.murt...@gmail.comwrote: 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 z6' (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 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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
