Re: [gmx-users] Problem with g_chi options
Hi! Thanks for your reply Justin! I have tried using a tpr file instead of a gro file, but that makes no difference. I still have the same problem! Does anybody have another idea? Thanks in advance! Anna On 07/09/2014 07:24 PM, Justin Lemkul wrote: On 7/9/14, 5:51 AM, Anna Stopka wrote: Hi everybody, I wrote last week, but nobody answered. So I write again, still having the same problem: I want do an analysis of my simulation with the tool g_chi. The problem is, that the optional output options don't work. I use the following command: g_chi -s config.gro -f traj.xtc -oh -all and all I get are the standard output files chi.log and order.xvg. I am not sure if it has something to do with the following warning I get: WARNING: not all dihedrals found in topology (only 1056 out of 1746)! Honestly, I don't understand why I get this warning, because all the input files are fine. Have you tried using a .tpr file instead of a .gro file as the structure passed to -s? I don't know how there can be any interpretation of a topology, given the fact that you haven't passed any topological information to g_chi. -Justin -- 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 gmx-users-requ...@gromacs.org.
[gmx-users] Problem with g_chi options
Hi everybody, I wrote last week, but nobody answered. So I write again, still having the same problem: I want do an analysis of my simulation with the tool g_chi. The problem is, that the optional output options don't work. I use the following command: g_chi -s config.gro -f traj.xtc -oh -all and all I get are the standard output files chi.log and order.xvg. I am not sure if it has something to do with the following warning I get: WARNING: not all dihedrals found in topology (only 1056 out of 1746)! Honestly, I don't understand why I get this warning, because all the input files are fine. Thanks for your help! Best regards, Anna -- 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 gmx-users-requ...@gromacs.org.
[gmx-users] Problem with g_chi options
Hi, I want do an analysis of my simulation with the tool g_chi. The problem is, that the optional output options don't work. I use the following command: g_chi -s config.gro -f traj.xtc -oh -all and all I get are the standard output files chi.log and order.xvg. I am not sure if it has something to do with the following warning I get: WARNING: not all dihedrals found in topology (only 1056 out of 1746)! Honestly, I don't understand why I get this warning, because all the input files are fine. Thanks for your help! Best regards, Anna -- 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 gmx-users-requ...@gromacs.org.
