Re: [gmx-users] xx of the xxxx bonded interactions couldn't be calculated
On 2013-06-07 04:12, Justin Lemkul wrote: On 6/6/13 10:00 PM, Badamkhatan wrote: Dear GMX-users Recently i got this error and note from my MD2 simulation. I'm solvating 1-octanol to 1-octanol and calculating free energy differences. This is the last step of my calculation and previous steps are looking fine. Basically i followed Justin's free energy tutorial. Here is Note: A list of missing interactions: LJC Pairs NB of210 missing 1 exclusions of 25308 missing 1 Molecule type '1-octanol' the first 10 missing interactions, except for exclusions: LJC Pairs NB atoms3 25 global 325 Fatal error: 2 of the 57736 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1 nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck Please help me and suggest any idea to solve this problem? Sounds like you're http://www.gromacs.org/Documentation/Terminology/Blowing_Up. It may also be the opposite, box shrinking under equilibration. Try: mdrun [options] -rdd 1.25 -Justin -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] xx of the xxxx bonded interactions couldn't be calculated
Dear GMX-users Recently i got this error and note from my MD2 simulation. I'm solvating 1-octanol to 1-octanol and calculating free energy differences. This is the last step of my calculation and previous steps are looking fine. Basically i followed Justin's free energy tutorial. Here is Note: A list of missing interactions: LJC Pairs NB of210 missing 1 exclusions of 25308 missing 1 Molecule type '1-octanol' the first 10 missing interactions, except for exclusions: LJC Pairs NB atoms3 25 global 325 Fatal error: 2 of the 57736 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1 nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck Please help me and suggest any idea to solve this problem? -- View this message in context: http://gromacs.5086.x6.nabble.com/xx-of-the--bonded-interactions-couldn-t-be-calculated-tp5008876.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] xx of the xxxx bonded interactions couldn't be calculated
On 6/6/13 10:00 PM, Badamkhatan wrote: Dear GMX-users Recently i got this error and note from my MD2 simulation. I'm solvating 1-octanol to 1-octanol and calculating free energy differences. This is the last step of my calculation and previous steps are looking fine. Basically i followed Justin's free energy tutorial. Here is Note: A list of missing interactions: LJC Pairs NB of210 missing 1 exclusions of 25308 missing 1 Molecule type '1-octanol' the first 10 missing interactions, except for exclusions: LJC Pairs NB atoms3 25 global 325 Fatal error: 2 of the 57736 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1 nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck Please help me and suggest any idea to solve this problem? Sounds like you're http://www.gromacs.org/Documentation/Terminology/Blowing_Up. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
