[gmx-users] g_hbond output
@ legend length 2 @ s0 legend Hydrogen bonds @ s1 legend Pairs within 0.35 nm 0 0 0 200 0 0 400 2 1 600 0 3 800 0 2 1000 1 0 : -- 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] g_hbond output
hi out there, still doing my first steps on the gmx planet. can anyone tell me, why there are 3 columns in the output file of g_hbond and how to interpret the output values when having run g_hbond -f mdNew.xtc -s md.tpr -num mdNew_numH.xvg first column frame! second column = #H bonds? third column = #all pairs within 0.35nm?? which pairs?? including all H bonds??? if yes, how can this value be less than the respective #H bonds for some frames? (see output below). i have counted the number of H bonds with vmd additionally (same angle and distance cut off), but they do not correlate with the ones here ... what am i doing wrong? output gmx: @title Hydrogen Bonds @xaxis label Time @yaxis label Number @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend Hydrogen bonds @ s1 legend Pairs within 0.35 nm 0 2 3 0.02 2 3 0.04 2 3 0.06 2 1 0.08 2 1 0.1 2 1 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 output
On 2010-03-17 16.26, vedat durmaz wrote: hi out there, still doing my first steps on the gmx planet. can anyone tell me, why there are 3 columns in the output file of g_hbond and how to interpret the output values when having run g_hbond -f mdNew.xtc -s md.tpr -num mdNew_numH.xvg first column frame! second column = #H bonds? third column = #all pairs within 0.35nm?? which pairs?? including all H bonds??? if yes, how can this value be less than the respective #H bonds for some frames? (see output below). Pairs that are not hbonded due to wrong angle. i have counted the number of H bonds with vmd additionally (same angle and distance cut off), but they do not correlate with the ones here ... what am i doing wrong? Definition (angle, cutoff) may be different. output gmx: @title Hydrogen Bonds @xaxis label Time @yaxis label Number @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend Hydrogen bonds @ s1 legend Pairs within 0.35 nm 0 2 3 0.02 2 3 0.04 2 3 0.06 2 1 0.08 2 1 0.1 2 1 -- 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/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 output analysis
[EMAIL PROTECTED] wrote: Message: 1 Date: Tue, 26 Aug 2008 15:38:56 +0530 (IST) From: [EMAIL PROTECTED] Subject: [gmx-users] g_hbond output analysis To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain;charset=iso-8859-1 hi i used the -num option for g_hbond run. since i new to gromacs i cannot able to interpret the output form. it comes in 3 columns with the first column indicating the frame, i dont know about the remaining two columns Kindly suggest Parthiban sundar -- Message: 2 Date: Tue, 26 Aug 2008 12:13:55 +0200 From: Florian Haberl [EMAIL PROTECTED] Subject: Re: [gmx-users] g_hbond output analysis To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=utf-8 Hi, On Tuesday, 26. August 2008, [EMAIL PROTECTED] wrote: hi i used the -num option for g_hbond run. since i new to gromacs i cannot able to interpret the output form. it comes in 3 columns with the first column indicating the frame, i dont know about the remaining two columns if you use g_hbond -h it tells you also if you have the legend inside the file (do not select -noxvgr) 2: Hydrogen bonds 3: Pairs within 0.35nm (depends on your select cutoff radius) Kindly suggest Parthiban sundar ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26573 Mailto: florian.haberl AT chemie.uni-erlangen.de --- Dear Florian other users can you pls. explain me in detail about the 3rd column in the g_hbond output in -num option it is the number of contacts, within the distance cut-off but not h-bonded. this is used in the HB kinetics analysis. Parthi sundar ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_hbond output analysis
hi i used the -num option for g_hbond run. since i new to gromacs i cannot able to interpret the output form. it comes in 3 columns with the first column indicating the frame, i dont know about the remaining two columns Kindly suggest Parthiban sundar ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_hbond output analysis
Hi, On Tuesday, 26. August 2008, [EMAIL PROTECTED] wrote: hi i used the -num option for g_hbond run. since i new to gromacs i cannot able to interpret the output form. it comes in 3 columns with the first column indicating the frame, i dont know about the remaining two columns if you use g_hbond -h it tells you also if you have the legend inside the file (do not select -noxvgr) 2: Hydrogen bonds 3: Pairs within 0.35nm (depends on your select cutoff radius) Kindly suggest Parthiban sundar ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26573 Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_hbond output analysis
Message: 1 Date: Tue, 26 Aug 2008 15:38:56 +0530 (IST) From: [EMAIL PROTECTED] Subject: [gmx-users] g_hbond output analysis To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain;charset=iso-8859-1 hi i used the -num option for g_hbond run. since i new to gromacs i cannot able to interpret the output form. it comes in 3 columns with the first column indicating the frame, i dont know about the remaining two columns Kindly suggest Parthiban sundar -- Message: 2 Date: Tue, 26 Aug 2008 12:13:55 +0200 From: Florian Haberl [EMAIL PROTECTED] Subject: Re: [gmx-users] g_hbond output analysis To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=utf-8 Hi, On Tuesday, 26. August 2008, [EMAIL PROTECTED] wrote: hi i used the -num option for g_hbond run. since i new to gromacs i cannot able to interpret the output form. it comes in 3 columns with the first column indicating the frame, i dont know about the remaining two columns if you use g_hbond -h it tells you also if you have the legend inside the file (do not select -noxvgr) 2: Hydrogen bonds 3: Pairs within 0.35nm (depends on your select cutoff radius) Kindly suggest Parthiban sundar ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) â 9131 â 85 26573 Mailto: florian.haberl AT chemie.uni-erlangen.de --- Dear Florian other users can you pls. explain me in detail about the 3rd column in the g_hbond output in -num option Parthi sundar ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
