[gmx-users] g_hbond error
Hello gmx-users !! I tried using g_hbond tool to analyse h-bonds on my system. I could successfully execute the tool for two of my systems. But the third system should the memory problem. Below I have pasted my command and its output. *$ g_hbond -s ../md0-20.tpr -f 40-50.trr -n index_2.ndx -num hbnum.xvg -dist hbdist.xvg -ang hbang.xvg -life hblife.xvg -nice 0 -xvgr No option -sel Reading file ../md0-20.tpr, VERSION 4.0.7 (single precision) Specify 2 groups to analyze: Group 0 ( System) has 95687 elements Group 1 ( HNP) has10 elements Group 2 ( PE) has 192 elements Group 3 ( HP) has 216 elements Group 4 ( CPE) has 9 elements Group 5 ( SOL) has 95235 elements Group 6 ( Cl) has25 elements Group 7 ( N_H) has 126 elements Select a group: 5 Selected 5: 'SOL' Select a group: 7 Selected 7: 'N_H' Checking for overlap in atoms between SOL and N_H Calculating hydrogen bonds between SOL (95235 atoms) and N_H (126 atoms) Found 31795 donors and 31795 acceptors --- Program g_hbond, VERSION 4.0.7 Source code file: smalloc.c, line: 147 Fatal error: Not enough memory. Failed to calloc 31795 elements of size 4 for hb-hbmap[i] (called from file gmx_hbond.c, line 186) --- I Solve Problems (Pulp Fiction) : Cannot allocate memory Making hbmap structure...* Kindly help. -- Chandan kumar Choudhury NCL, Pune INDIA -- 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_hbond error
Justin A. Lemkul skrev: krishnakumar wrote: Hi, Has any one encountered this error while using g_hbond? * Select a group: 12 Selected 12: 'SOL' Select a group: 12 Selected 12: 'SOL' Calculating hydrogen bonds in SOL (20949 atoms) --- Program g_hbond, VERSION 4.0.4 Source code file: gmx_hbond.c, line: 565 Fatal error: Error in func_type Position Rest. --- I get this error only when using trajectory with positional restraint during MD. Is there any fix for this bug? Probably not, unless you submit a bugzilla :) The search page is not working properly due to the website migration, so it might be hard to determine if anyone else has reported such a problem. It may be due to the fact that typical use of position restraints is for equilibration, with the PR time period getting discarded (not analyzed). Thus, you are doing an analysis that was unforeseen. If you want to analyze this portion of the trajectory, you could create a new .tpr file (identical to your original, but without defining position restraints in the .mdp file), and trying to run the analysis again. If that alleviates the problem, it would be useful to include as part of a bugzilla report. -Justin Agreed. That ought to work. I have an idea of what the problem might be, and it should be a fairly easy fix. Still, a bugzilla will prevent me or someone else from forgetting about it, so please submit one. /Erik Thanks Krishna ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] g_hbond error
Hi, Has any one encountered this error while using g_hbond? * Select a group: 12 Selected 12: 'SOL' Select a group: 12 Selected 12: 'SOL' Calculating hydrogen bonds in SOL (20949 atoms) --- Program g_hbond, VERSION 4.0.4 Source code file: gmx_hbond.c, line: 565 Fatal error: Error in func_type Position Rest. --- I get this error only when using trajectory with positional restraint during MD. Is there any fix for this bug? Thanks Krishna ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] g_hbond error
krishnakumar wrote: Hi, Has any one encountered this error while using g_hbond? * Select a group: 12 Selected 12: 'SOL' Select a group: 12 Selected 12: 'SOL' Calculating hydrogen bonds in SOL (20949 atoms) --- Program g_hbond, VERSION 4.0.4 Source code file: gmx_hbond.c, line: 565 Fatal error: Error in func_type Position Rest. --- I get this error only when using trajectory with positional restraint during MD. Is there any fix for this bug? Probably not, unless you submit a bugzilla :) The search page is not working properly due to the website migration, so it might be hard to determine if anyone else has reported such a problem. It may be due to the fact that typical use of position restraints is for equilibration, with the PR time period getting discarded (not analyzed). Thus, you are doing an analysis that was unforeseen. If you want to analyze this portion of the trajectory, you could create a new .tpr file (identical to your original, but without defining position restraints in the .mdp file), and trying to run the analysis again. If that alleviates the problem, it would be useful to include as part of a bugzilla report. -Justin Thanks Krishna ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] g_hbond error Your computational box has shrunk too much
Hi all, I'm beginning to analyze my trajectories, everything works fine with (g_rmsf, g_saltbr ...) but when i try to use g_hbond I receive this error: -- Program g_hbond, VERSION 3.3.1 Source code file: gmx_hbond.c, line: 631 Fatal error: Your computational box has shrunk too much. g_hbond can not handle this situation, sorry. --- Is this a bug or a problme with my system? Is there the possibility to avoid this problem in some way? THANKS Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
