Re: [gmx-users] Re: Simulating a semi-membrane protein
Dear Pavithrakb, First of all, your choice will depend on the available parameters for the lipid molecules that you want to simulate (check the Lipidbook repositoryhttp://lipidbook.bioch.ox.ac.uk/ ). Concerning the GROMOS force fields the most recent lipid parameters are the ones included in the G54A8 force field (Reif_2012_JCTC_8_3705, Reif_2013_JCTC_9_1247). However, Poger et al proposed an add-on to the standard G53A6 (Poger_2010_JCC_31_1117 and Poger_2010_JCTC_6_325), lately incorporated in the G54A7 (Schmidt_2011_EBJ_40_843), that is commonly used and yields good results for the analysed lipid parameters (i.e. in agreement with experimental measurements). Despite the aforementioned papers, you might want to go through the references listed bellow concerning several lipid parameters for GROMOS force fields or proposed modifications (e.g. cutoff schemes, charges, charge group distributions): - Berger lipids: Berger_1997_JB_72_2010 - Ash lipids: Tieleman_2006_JPCM_18_S1221 - G43A1-S3: Chiu_2009_JPCB_113_2748 - G45A3: Schuler_2001_JCC_22_1205, Chandrasekhar_2003_EBJ_32_67 - Modified Berger: Anezo_2003_JPCB_107_9424 - Modified ffG45A3: Anezo_2003_JPCB_107_9424 - Kukol lipids: Kukol_2009_JCTC_5_615 - G53A6L: Poger_2010_JCC_31_1117, Poger_2010_JCTC_6_325 - G54A7: Schmidt_2011_EBJ_40_843 - G54A8: Reif_2012_JCTC_8_3705, Reif_2013_JCTC_9_1247 -- Catarina Santos Research Student Molecular Simulation Group Instituto de Tecnologia Química e Biológica Universidade Nova de Lisboa Av.da República, Apartado 127 2781-901 Oeiras, Portugal -- 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] LAMBADA and InflateGRO2
Hi Atila, Lambada was not able to properly identify the membrane reference atoms and you get that error message when it tries to calculate the membrane centre in the Z-axis. Although I'm not an expert I would recommend you to use an index file for the protein and the membrane (options -n1 and -n2, type lambada -h). In my case this was the solution to that problem, but my system is simpler than yours. -- Catarina Santos Research Student Molecular Simulation Group Instituto de Tecnologia Química e Biológica Universidade Nova de Lisboa Av.da República, Apartado 127 2781-901 Oeiras, Portugal -- 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] Furthest distance between 2 atoms
Hi everybody, I am trying to find an easy way to calculate the furthest distance between the atoms of two groups in a system. I know that g_dist can give me all the distances I want, but I would have to run g_dist for each possible atom pair (which is not a fast or a straightforward process). I have already checked the manual and tried some tools, I did not find anything that returns all the distances between all the possible pairs of atoms though. Am I missing something? Thanks in advance. Regards, Catarina Santos Research Student Molecular Simulation Group Instituto de Tecnologia Química e Biológica Universidade Nova de Lisboa Av.da República, Apartado 127 2781-901 Oeiras, Portugal -- 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
