[gmx-users] Re: g_hbond
Hi, Erik Thank you very much!Thank you! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/g-hbond-tp5008507p5008548.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
[gmx-users] Re: g_hbond
Hi, Pan Thank you very much for your kind help! Thank you! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/g-hbond-tp5008507p5008513.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
[gmx-users] about g_hbond
Hi all, When calculating the average number of hbonds during a simulation, does the program g_hbond contemplate the possibility of an atom involved in two hbond? If I visualize the structures with molden, setting the same cutoff criterion for hbonding than g_hbond utilizes, I found out that some O atoms are forming two H bonds with two different hydrogen atoms at once. Other O atoms are forming just one H bond. With g_hbond I get the same average on systems when the same O atoms are forming two hbonds and in those where they form just one. If the criterion is just a cutoff distance and angle, I guess I should have seen the differences when using g_hbond with -num, but this never happened... Any clue? -- 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] about g_hbond
On 1/11/13 6:23 AM, Miguel Ángel Mompeán García wrote: Hi all, When calculating the average number of hbonds during a simulation, does the program g_hbond contemplate the possibility of an atom involved in two hbond? If I visualize the structures with molden, setting the same cutoff criterion for hbonding than g_hbond utilizes, I found out that some O atoms are forming two H bonds with two different hydrogen atoms at once. Other O atoms are forming just one H bond. With g_hbond I get the same average on systems when the same O atoms are forming two hbonds and in those where they form just one. If the criterion is just a cutoff distance and angle, I guess I should have seen the differences when using g_hbond with -num, but this never happened... Any clue? For O atoms with two putative H-bonds, are the donors on separate functional groups or molecules? If they are not, g_hbond considers them the same, since that is the default behavior of the -merge option. If you specify -nomerge, then the two hydrogen bonds will be considered distinct. -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
[gmx-users] about g_hbond
Hi all, When calculating the average number of hbonds during a simulation, does the program g_hbond contemplate the possibility of an atom involved in two hbond? If I visualize the structures with molden, setting the same cutoff criterion for hbonding than g_hbond utilizes, I found out that some O atoms are forming two H bonds with two different hydrogen atoms at once. Other O atoms are forming just one H bond. With g_hbond I get the same average on systems when the same O atoms are forming two hbonds and in those where they form just one. If the criterion is just a cutoff distance and angle, I guess I should have seen the differences when using g_hbond with -num, but this never happened... Any clue? -- 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] about g_hbond
The donors are two H atoms from the amide group of Gln residues. Thus, I will try the -merge option. Thank for the comment. I wonder if the following issue is affecting gromacs 4.5.5: http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html 2013/1/11, Justin Lemkul jalem...@vt.edu: On 1/11/13 6:23 AM, Miguel Ángel Mompeán García wrote: Hi all, When calculating the average number of hbonds during a simulation, does the program g_hbond contemplate the possibility of an atom involved in two hbond? If I visualize the structures with molden, setting the same cutoff criterion for hbonding than g_hbond utilizes, I found out that some O atoms are forming two H bonds with two different hydrogen atoms at once. Other O atoms are forming just one H bond. With g_hbond I get the same average on systems when the same O atoms are forming two hbonds and in those where they form just one. If the criterion is just a cutoff distance and angle, I guess I should have seen the differences when using g_hbond with -num, but this never happened... Any clue? For O atoms with two putative H-bonds, are the donors on separate functional groups or molecules? If they are not, g_hbond considers them the same, since that is the default behavior of the -merge option. If you specify -nomerge, then the two hydrogen bonds will be considered distinct. -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 -- 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] about g_hbond
On 1/11/13 1:10 PM, Miguel Ángel Mompeán García wrote: The donors are two H atoms from the amide group of Gln residues. Thus, I will try the -merge option. Thank for the comment. I wonder if the following issue is affecting gromacs 4.5.5: http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html No, that issue was fixed before the 4.5.5 release. -Justin 2013/1/11, Justin Lemkul jalem...@vt.edu: On 1/11/13 6:23 AM, Miguel Ángel Mompeán García wrote: Hi all, When calculating the average number of hbonds during a simulation, does the program g_hbond contemplate the possibility of an atom involved in two hbond? If I visualize the structures with molden, setting the same cutoff criterion for hbonding than g_hbond utilizes, I found out that some O atoms are forming two H bonds with two different hydrogen atoms at once. Other O atoms are forming just one H bond. With g_hbond I get the same average on systems when the same O atoms are forming two hbonds and in those where they form just one. If the criterion is just a cutoff distance and angle, I guess I should have seen the differences when using g_hbond with -num, but this never happened... Any clue? For O atoms with two putative H-bonds, are the donors on separate functional groups or molecules? If they are not, g_hbond considers them the same, since that is the default behavior of the -merge option. If you specify -nomerge, then the two hydrogen bonds will be considered distinct. -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 -- 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
[gmx-users] On g_hbond
Hi everyone! On this page http://manual.gromacs.org/online/g_hbond.html there is an option -r2 when using g_hbond. What is this r2? I can't find it in the Gromacs manual. option -a is the angle H-O-O, option -r is the O-O distance which can be switched to H-A by using the -da no. Need help on what is -r2 (could this be for specifying a third criterion for the for distance O-H in addition to the angle cut-off and O-O distance cut-off). Thanks! Bernard-- 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] reg g_hbond
Dear Justin, Thank you for your previous reply Dear Justin I used g_hbond tool i have got .xvg file In that file there are three column The second and third colum represents What ?. Which column represents total no of Hbonds throught the entire trajectory and which Columns represents Average number of H bonds Thanks in Advance -- 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] reg g_hbond
On 19/06/2011 11:44 PM, vidhya sankar wrote: Dear Justin, Thank you for your previous reply Dear Justin I used g_hbond tool i have got .xvg file In that file there are three column The second and third colum represents What ?. Which column represents total no of Hbonds throught the entire trajectory and which Columns represents Average number of H bonds Thanks in Advance Look at the legend text in the .xvg file. Also, try Google before emailing - often fruitful: http://www.google.com.au/search?sourceid=chromeie=UTF-8q=gromacs+g_hbond+output http://www.google.com.au/search?sourceid=chromeie=UTF-8q=gromacs+g_hbond+output Mark -- 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] about g_hbond
I got it. I should have outputted the -hbn file.
Thanks,
On Thu, May 12, 2011 at 1:09 PM, lina lina.lastn...@gmail.com wrote:
/* y-label: Hydrogen Bond Index */
is it relevant to the total number of hydrogen bonds?
such as
/* XPM */
/* x-label: Time (ps) */
/* y-label: Hydrogen Bond Index */
/* type: Discrete */
static char *gromacs_xpm[] = {
A-b : 51 84 2 1,
b-C : 51 95 2 1,
84, 95?
Thanks,
On Wed, May 11, 2011 at 11:10 PM, Justin A. Lemkul jalem...@vt.edu wrote:
lina wrote:
Hi,
For group A, b, C.
It's no doubt can get hb forming number between A-b, b-C. b-(A or C).
But I don't know how to get the number of residues of b forming both
with A and B at the same time. namely b-AC, not with AC group.
There's no direct way to do it, but from the output files of g_hbond it can
be done. You'd need the .xpm files of A-C and B-C hydrogen bonds, and write
some script that parses the .xpm files, and whenever there is an entry of
A-C in the same frame as B-C, then you have a hydrogen bond mediated between
the two.
There's lots of discussion in the list archive about water-mediated
hydrogen bonds that is likely applicable here.
Note that if you're using g_hbond in version 4.5, there is an important bug
that was fixed just yesterday:
http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html
-Justin
Thanks,
--
Best Regards,
lina
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
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--
Best Regards,
lina
--
Best Regards,
lina
--
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[gmx-users] about g_hbond
Hi, For group A, b, C. It's no doubt can get hb forming number between A-b, b-C. b-(A or C). But I don't know how to get the number of residues of b forming both with A and B at the same time. namely b-AC, not with AC group. Thanks, -- Best Regards, lina -- Best Regards, lina -- 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] about g_hbond
lina wrote: Hi, For group A, b, C. It's no doubt can get hb forming number between A-b, b-C. b-(A or C). But I don't know how to get the number of residues of b forming both with A and B at the same time. namely b-AC, not with AC group. There's no direct way to do it, but from the output files of g_hbond it can be done. You'd need the .xpm files of A-C and B-C hydrogen bonds, and write some script that parses the .xpm files, and whenever there is an entry of A-C in the same frame as B-C, then you have a hydrogen bond mediated between the two. There's lots of discussion in the list archive about water-mediated hydrogen bonds that is likely applicable here. Note that if you're using g_hbond in version 4.5, there is an important bug that was fixed just yesterday: http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html -Justin Thanks, -- Best Regards, lina -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
Re: [gmx-users] about g_hbond
/* y-label: Hydrogen Bond Index */
is it relevant to the total number of hydrogen bonds?
such as
/* XPM */
/* x-label: Time (ps) */
/* y-label: Hydrogen Bond Index */
/* type:Discrete */
static char *gromacs_xpm[] = {
A-b : 51 84 2 1,
b-C : 51 95 2 1,
84, 95?
Thanks,
On Wed, May 11, 2011 at 11:10 PM, Justin A. Lemkul jalem...@vt.edu wrote:
lina wrote:
Hi,
For group A, b, C.
It's no doubt can get hb forming number between A-b, b-C. b-(A or C).
But I don't know how to get the number of residues of b forming both
with A and B at the same time. namely b-AC, not with AC group.
There's no direct way to do it, but from the output files of g_hbond it can
be done. You'd need the .xpm files of A-C and B-C hydrogen bonds, and write
some script that parses the .xpm files, and whenever there is an entry of
A-C in the same frame as B-C, then you have a hydrogen bond mediated between
the two.
There's lots of discussion in the list archive about water-mediated
hydrogen bonds that is likely applicable here.
Note that if you're using g_hbond in version 4.5, there is an important bug
that was fixed just yesterday:
http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html
-Justin
Thanks,
--
Best Regards,
lina
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
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--
Best Regards,
lina
--
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[gmx-users] Re: g_hbond error
I missed my Gromacs version. It's 4.0.7 -- Chandan kumar Choudhury NCL, Pune INDIA On Wed, Apr 13, 2011 at 4:58 PM, Chandan Choudhury iitd...@gmail.comwrote: 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] Re: g_hbond error
Certain options require an amount of memory that is proportional to na x nd x t, where na and nd are number of acceptors and donors, and t is time. You need more memory. Or you could do your calculation for a subset of your solvent. Erik Chandan Choudhury skrev 2011-04-13 13.29: I missed my Gromacs version. It's 4.0.7 -- Chandan kumar Choudhury NCL, Pune INDIA On Wed, Apr 13, 2011 at 4:58 PM, Chandan Choudhury iitd...@gmail.com mailto:iitd...@gmail.com wrote: 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 -- --- Erik Marklund, PhD student 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://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
Re: [gmx-users] Re: g_hbond output
If I understand correctly, $2 is the number of hydrogen bonds defined by cutoff distance and the cutoff angle. $3 is the number of pairs within the cutoff distance, but beyond the cutoff angle. You may got different number of hbonds using different cutoff distance and cutoff angle. Jianguo From: ZHAO Lina lnzha...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, 16 March 2011 13:33:57 Subject: [gmx-users] Re: 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 : 5 3 2 Here the situations, what's the $2 and $3 mean, why when $1=1000, $3=0 if the $3 means pairs. I tried pymol, and on the last frame, there were 4 hydrogen bonds, between 7 residues. it's different from here 3 2 Thanks and sorry for last email without my realization it sent. lina -- 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] Re: g_hbond output
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 Here is my question, since there is already one bond formed, then why there is none pairs in 1000? On Wed, Mar 16, 2011 at 3:16 PM, Jianguo Li ljg...@yahoo.com.sg wrote: If I understand correctly, $2 is the number of hydrogen bonds defined by cutoff distance and the cutoff angle. $3 is the number of pairs within the cutoff distance, but beyond the cutoff angle. You may got different number of hbonds using different cutoff distance and cutoff angle. Jianguo -- *From:* ZHAO Lina lnzha...@gmail.com *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wednesday, 16 March 2011 13:33:57 *Subject:* [gmx-users] Re: 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 : 5 3 2 Here the situations, what's the $2 and $3 mean, why when $1=1000, $3=0 if the $3 means pairs. I tried pymol, and on the last frame, there were 4 hydrogen bonds, between 7 residues. it's different from here 3 2 Thanks and sorry for last email without my realization it sent. lina -- 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 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] Re: g_hbond output
A pair within the cutoff distance (e.g., 0.35nm) either belongs to $2 or $3, but cannot belong to both columns. If the program finds a pair shorter than 0.35nm, and the angle is smaller than 30deg., then the program put this pair in the column 2. If the program finds a pair shorter than 0.35nm, and the angle is larger than 30deg., then the program put this pair in the column 3. Jianguo From: ZHAO Lina lnzha...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, 16 March 2011 15:31:30 Subject: Re: [gmx-users] Re: g_hbond output 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 Here is my question, since there is already one bond formed, then why there is none pairs in 1000? On Wed, Mar 16, 2011 at 3:16 PM, Jianguo Li ljg...@yahoo.com.sg wrote: If I understand correctly, $2 is the number of hydrogen bonds defined by cutoff distance and the cutoff angle. $3 is the number of pairs within the cutoff distance, but beyond the cutoff angle. You may got different number of hbonds using different cutoff distance and cutoff angle. Jianguo From: ZHAO Lina lnzha...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, 16 March 2011 13:33:57 Subject: [gmx-users] Re: 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 : 5 3 2 Here the situations, what's the $2 and $3 mean, why when $1=1000, $3=0 if the $3 means pairs. I tried pymol, and on the last frame, there were 4 hydrogen bonds, between 7 residues. it's different from here 3 2 Thanks and sorry for last email without my realization it sent. lina -- 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 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] Re: g_hbond output
ZHAO Lina skrev 2011-03-16 06.33: @ 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 : 5 3 2 Here the situations, what's the $2 and $3 mean, why when $1=1000, $3=0 if the $3 means pairs. I tried pymol, and on the last frame, there were 4 hydrogen bonds, between 7 residues. it's different from here 3 2 Last time I checked there's no hbond tool in pymol (although that may have changed without me knowing it). I have seen scrpts that does it for you, but they didn't take angles into account. Hence, different criteria may explain the discrepancy. Thanks and sorry for last email without my realization it sent. lina -- --- Erik Marklund, PhD student 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://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
Re: [gmx-users] Re: g_hbond output
Erik Marklund skrev 2011-03-16 16.25: ZHAO Lina skrev 2011-03-16 06.33: @ 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 : 5 3 2 Here the situations, what's the $2 and $3 mean, why when $1=1000, $3=0 if the $3 means pairs. I tried pymol, and on the last frame, there were 4 hydrogen bonds, between 7 residues. it's different from here 3 2 Last time I checked there's no hbond tool in pymol (although that may have changed without me knowing it). I have seen scrpts that does it for you, but they didn't take angles into account. Hence, different criteria may explain the discrepancy. I should add that there are issues with the current version of g_hbond, and I'm trying to find the time to fix them, but I'm in the process of finalizing my thesis, so I won't do it right away. Thanks and sorry for last email without my realization it sent. lina -- --- Erik Marklund, PhD student 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://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] Re: 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 : 5 3 2 Here the situations, what's the $2 and $3 mean, why when $1=1000, $3=0 if the $3 means pairs. I tried pymol, and on the last frame, there were 4 hydrogen bonds, between 7 residues. it's different from here 3 2 Thanks and sorry for last email without my realization it sent. lina -- 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] Re: g_hbond modification
Thanks for the prompt reply Justin, but I'm still not convinced that I can extract the information I seek from the g_hbond program without modification. I realize this wasn't clear in my initial message: I would like to know how many OH donors are not participating in ANY hydrogen bonds. If I calculate the number of non-hydrogen bound OH donors as the difference between the number of pairs that meet the distance requirement, and the actual number of hydrogen bonds (column 3 minus column 2 in hbnum), then I would be over-counting, as this does not exclude pairs with OH donors that are also included in a hydrogen bond with another O acceptor. Robin Quoting Robin C. Underwood rcund...@purdue.edu: I would like to modify the g_hbond code (or preferably, know how to implement g_hbond if it is already capable) to count the number of non-hydrogen bound water OH donors in a simulation. I define a non-hydrogen bound donor as one that does not meet the distance requirement, or one that may meet the distance requirement for a hydrogen bond, but does not meet the angle requirement. An inferred value of non-hydrogen bound OH donors is not exact because there is not a rigorously defined maximum value for the number of hydrogen bonds per water, (e.g. a single OH donor may qualify as part of a hydrogen bond at two adjacent water's O-acceptor sites, making the maximum possible number of hydrogen bonds for the water of this particular OH donor greater than 4). Is there a way to implement g_hbond to do this? If not, any specific information on what to consider, and how to modify the g_hbond source code to count non-hydrogen bound water OH donors is greatly appreciated. Robin -- Robin C. Underwood Chemistry Department 560 Oval Drive West Lafayette, IN 47907 -- Robin C. Underwood Chemistry Department 560 Oval Drive West Lafayette, IN 47907 -- 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] Re: g_hbond modification
Hi, Robin. I think it could be extracted using the -hbm and -hbn output (pretty much everything can). Write a python script that reads the files and checks which donors don't participate in hbonds at each frame. Alternatively, if you want to hack gmx_hbond.c, i suggest the following: Use the t_donors struct in (hb-d in gmx_hbond()) to create an bolean array with one element per donor (or donor+H depending on what you want to know in the end). Then set each element to TRUE whenever that donor is acting as a hydrogen bond donor. At the end of each frame just go through the array and write the number of non-donors to file. Clear the array and attack next frame. Erik Robin C. Underwood skrev 2010-11-08 22.10: Thanks for the prompt reply Justin, but I'm still not convinced that I can extract the information I seek from the g_hbond program without modification. I realize this wasn't clear in my initial message: I would like to know how many OH donors are not participating in ANY hydrogen bonds. If I calculate the number of non-hydrogen bound OH donors as the difference between the number of pairs that meet the distance requirement, and the actual number of hydrogen bonds (column 3 minus column 2 in hbnum), then I would be over-counting, as this does not exclude pairs with OH donors that are also included in a hydrogen bond with another O acceptor. Robin Quoting Robin C. Underwoodrcund...@purdue.edu: I would like to modify the g_hbond code (or preferably, know how to implement g_hbond if it is already capable) to count the number of non-hydrogen bound water OH donors in a simulation. I define a non-hydrogen bound donor as one that does not meet the distance requirement, or one that may meet the distance requirement for a hydrogen bond, but does not meet the angle requirement. An inferred value of non-hydrogen bound OH donors is not exact because there is not a rigorously defined maximum value for the number of hydrogen bonds per water, (e.g. a single OH donor may qualify as part of a hydrogen bond at two adjacent water's O-acceptor sites, making the maximum possible number of hydrogen bonds for the water of this particular OH donor greater than 4). Is there a way to implement g_hbond to do this? If not, any specific information on what to consider, and how to modify the g_hbond source code to count non-hydrogen bound water OH donors is greatly appreciated. Robin -- Robin C. Underwood Chemistry Department 560 Oval Drive West Lafayette, IN 47907 -- --- Erik Marklund, PhD student 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://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
Re: [gmx-users] Re: g_hbond modification
On 2010-11-08 22.10, Robin C. Underwood wrote: Thanks for the prompt reply Justin, but I'm still not convinced that I can extract the information I seek from the g_hbond program without modification. I realize this wasn't clear in my initial message: I would like to know how many OH donors are not participating in ANY hydrogen bonds. check out the -nhbdist flag. If I calculate the number of non-hydrogen bound OH donors as the difference between the number of pairs that meet the distance requirement, and the actual number of hydrogen bonds (column 3 minus column 2 in hbnum), then I would be over-counting, as this does not exclude pairs with OH donors that are also included in a hydrogen bond with another O acceptor. Robin Quoting Robin C. Underwoodrcund...@purdue.edu: I would like to modify the g_hbond code (or preferably, know how to implement g_hbond if it is already capable) to count the number of non-hydrogen bound water OH donors in a simulation. I define a non-hydrogen bound donor as one that does not meet the distance requirement, or one that may meet the distance requirement for a hydrogen bond, but does not meet the angle requirement. An inferred value of non-hydrogen bound OH donors is not exact because there is not a rigorously defined maximum value for the number of hydrogen bonds per water, (e.g. a single OH donor may qualify as part of a hydrogen bond at two adjacent water's O-acceptor sites, making the maximum possible number of hydrogen bonds for the water of this particular OH donor greater than 4). Is there a way to implement g_hbond to do this? If not, any specific information on what to consider, and how to modify the g_hbond source code to count non-hydrogen bound water OH donors is greatly appreciated. Robin -- Robin C. Underwood Chemistry Department 560 Oval Drive West Lafayette, IN 47907 -- 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] Fw: g_hbond segmentation fault
-- Found 1048 different hydrogen bonds in trajectory Found 2292 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 2/10915Segmentation fault __ Hi guys, I got the msg like above when I ran g_hbond in version 4.5. Any guess on the problem? Thanks, Yao -- 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] Fw: g_hbond segmentation fault
Yao Yao skrev 2010-09-28 19.25: -- Found 1048 different hydrogen bonds in trajectory Found 2292 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 2/10915Segmentation fault __ Hi guys, I got the msg like above when I ran g_hbond in version 4.5. Any guess on the problem? Thanks, Yao And I replied and asked you what was the command line. -- --- Erik Marklund, PhD student 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://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
Re: [gmx-users] Fw: g_hbond segmentation fault
Hi Erik, Sorry about that, I did not notice it. I used the command line, g_hbond -f test.trr -s test.tpr -ac test.xvg -e 100 -dt 1 Thanks, Yao --- On Tue, 9/28/10, Erik Marklund er...@xray.bmc.uu.se wrote: From: Erik Marklund er...@xray.bmc.uu.se Subject: Re: [gmx-users] Fw: g_hbond segmentation fault To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, September 28, 2010, 6:22 PM Yao Yao skrev 2010-09-28 19.25: -- Found 1048 different hydrogen bonds in trajectory Found 2292 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 2/10915Segmentation fault __ Hi guys, I got the msg like above when I ran g_hbond in version 4.5. Any guess on the problem? Thanks, Yao And I replied and asked you what was the command line. -- --- Erik Marklund, PhD student 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.se http://folding.bmc.uu.se/ -Inline Attachment Follows- -- gmx-users mailing list gmx-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 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] different g_hbond result for two run
hi all, I was trying to analyze some h_bond interaction for a protein with one ligand. I tried two runs for the same one for 5 nsec and another for 10 nsec. What I found here is that, the h-bonds present in the 5 nsec trajectory are more than that in 10 nsec trajectory, h-bonds in 10 nsec run should be at least equal to that in 5 nsec run. for the two trajectory i have taken out the 10 frames. are the interaction picked up by g_hbond are dependent on the full trajectory or the frames only. whether the two different run on the same input file with same parameter can be related or compared ? Can anybody help me in the same case by giving some explanation or giving right way to do it ? With Thanks, VIVEk ___ 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] Re: g_hbond in version 3.4.1 vs rest (Especially higher one)
Anil Kumar wrote: Dear Justin, Sorry for sending personal email regarding the query related to gromacs. Actually long back i had send this query many times on forum but didn't got any reply. Nevertheless, I don't solicit extra work. Please keep all Gromacs-related questions on the mailing list. The risk you take is that the person from whom you're asking advice has no idea what the problem is. That is the case here. I have never had a need to use g_hbond -hx, so I have no idea what the problem is. It sounds like there *may* be some problem with this option in newer versions of Gromacs, but that is pure speculation. If you can show output from each version to compare, that would be useful, clearly indicating the version of Gromacs used to obtain each, along with the *exact* command line used to produce the output, maybe that will be illustrative to someone who knows more than I. Be sure to also describe how each version of Gromacs was compiled. As described repeatedly on the gmx-users list, using gcc-4.1.x often causes analysis tools (among others) to produce strange results. -Justin When i use g_hbond with -hx option to know the pattern of hydrogen bond then i got very surprising result in higher version (3.2.1/3.3.1 etc0 with output under n-n column (which is illogical!). Earlier i was using 3.4.1 and here i never come across this kind of strange hydrogen bond. Would you kindly let me know where is the problem! Even i had tried g_hbond with same PDB on 3.4.1 and higher...in case of 3.4.1 it gives correct hydrogen bond pattern...but in higher version it shows hydrogen bonds under n-n column. Your expert comments will be highly appreciated. Waiting for kind response. Thanks, With Warm Regards - ANIL KUMAR(Senior Research Scholar) | Graduate Student of Prof. S. Durani's Research Group | Bio-Organic Lab No-336(2nd Floor), | Dept. of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai-400076, Ph. No.+91-22-25764780 (Lab) +91-22-25764168 (Lab) Fax: +91-22-25767152 - Residence:- Hostel#1,Room#297, I.I.T. Bombay, Powai,Mumbai-400076, Ph.No.:-+91-9819638547 (Mobile) - Web:http://chemanil.googlepages.com/ - Education is a progressive discovery of our ignorance - Will Durant -- Justin A. Lemkul Graduate Research Assistant 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: g_hbond error Your computational box has shrunk too much
andrea carotti wrote: Is it correct? Did you plot the box volume as a function of time? You can use g_hbond for different stretches of the trajectory and combine the results manually. -- Thanks for the fast reply. I'm only trying to monitor the hbond formation with the basic command g_hbond -f m93_newtraj.trr -s topol.tpr -n and giving to the groups selection two different parts of my protein (i've made an index file)..and then the programs suddenly stop. the default output (-num) should be the total number of hbond per frame. Please help me again Andrea you haven't answered my question, and haven't read my advice either. ___ 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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 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] Re: g_hbond error Your computational box has shrunk too much
andrea carotti wrote: The problem is that i don't have an energy file cause this time I'm using gromacs only for analyze my trajs...so I don't know how to make the plot you suggested. Now perhaps I've found a workaroud using trjconv with the option -box 1 1 1 set, but I' don't know if this could be correct. make it a realistic size, maybe 3 3 3 (I've checked the ouput traj in VMD and seems fine, and with it g_hbond is working) Best 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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 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] Re: g_hbond
Jian Zou wrote:
Hi David,
I read your JPCB paper (JPCB-110-4393) and it says that the geometric
criteria with DA distance and DHA angle is employed. Therefore I'm a little
confused which angle is indeed used to determine the Hbond, HDA or DHA?
Oops, that is wrong in the paper! It is HDA in the program.
In the literature, e.g. the two papers by Starr et al. and the paper by
Xu Berne it is said that the O-H ... O should be less then thirty
degrees, which is also what I wrote in my paper (DHA) however that does
not make sense, because that angle is more than 90 degrees in a HB.
Sorry about the confusion, but I'm sure that everyone either uses HDA or
HAD. We can reproduce exactly the numbers of Xu Berne with g_hbond for
TIP4P and SPC/E.
Regards,
Jian Zou
David van der Spoel wrote:
Dear David,
ok. Now I understand HDA criterion. Can you give me a reference
where I can find the differences between HDA criteria and OHD criteria
and why one of them is preferable than the other?
We implemented this in order to reproduce a number of publications. It
is difficult to say that one is to be preferred over the other. If
something an energy-based criterium could be preferred, however
classical mechanics is not good enough to quantitatively describe the
details of hydrogen bonding anyway. Some interesting refs are:
@Article{Starr2000a,
author = {F. W. Starr and J. K. Nielsen and H. Eugene Stanley},
title = {Hydrogen-bond dynamics for the extended simple point
charge model of water},
journal = {Phys. Rev. E},
year = 2000,
volume = 62,
pages = {579-587}
}
@Article{Modig2003a,
author = {K. Modig and B. G. Pfrommer and B. Halle},
title = {Temperature-dependent hydrogen bond geometry in liquid water},
journal = {Phys. Rev. Lett.},
year = 2003,
volume = 90,
pages = 075502
}
@Article{Spoel2006b,
author = {D. van der Spoel and P. J. van Maaren and P. Larsson and
N. Timneanu},
title = {Thermodynamics of hydrogen bonding in hydrophilic and
hydrophobic media},
journal = {J. Phys. Chem. B},
year = 2006,
volume = 110,
pages = {4393-4398}
}
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--
David.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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[gmx-users] Re: g_hbond
Hi David,
I read your JPCB paper (JPCB-110-4393) and it says that the geometric
criteria with DA distance and DHA angle is employed. Therefore I'm a little
confused which angle is indeed used to determine the Hbond, HDA or DHA?
Regards,
Jian Zou
David van der Spoel wrote:
Dear David,
ok. Now I understand HDA criterion. Can you give me a reference
where I can find the differences between HDA criteria and OHD criteria
and why one of them is preferable than the other?
We implemented this in order to reproduce a number of publications. It
is difficult to say that one is to be preferred over the other. If
something an energy-based criterium could be preferred, however
classical mechanics is not good enough to quantitatively describe the
details of hydrogen bonding anyway. Some interesting refs are:
@Article{Starr2000a,
author = {F. W. Starr and J. K. Nielsen and H. Eugene Stanley},
title = {Hydrogen-bond dynamics for the extended simple point
charge model of water},
journal = {Phys. Rev. E},
year = 2000,
volume = 62,
pages = {579-587}
}
@Article{Modig2003a,
author = {K. Modig and B. G. Pfrommer and B. Halle},
title = {Temperature-dependent hydrogen bond geometry in liquid water},
journal = {Phys. Rev. Lett.},
year = 2003,
volume = 90,
pages = 075502
}
@Article{Spoel2006b,
author = {D. van der Spoel and P. J. van Maaren and P. Larsson and
N. Timneanu},
title = {Thermodynamics of hydrogen bonding in hydrophilic and
hydrophobic media},
journal = {J. Phys. Chem. B},
year = 2006,
volume = 110,
pages = {4393-4398}
}
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Re: [gmx-users] Re: g_hbond
Well,this was my command line:g_hbond -f ../../traj_c.trr -s ../../topol.tpr -g -num -dist -ang -hbn and this was my screen output No option -daReading file ../../topol.tpr, VERSION 3.2.1 (single precision)Specify 2 groups to analyze:Opening library file /usr/local/share/gromacs/top/aminoacids.dat Group 0 ( System) has 25707 elementsGroup 1 ( Protein) has 2462 elementsGroup 2 ( Protein-H) has 1975 elementsGroup 3 ( C-alpha) has 247 elementsGroup 4 ( Backbone) has 741 elements Group 5 ( MainChain) has 989 elementsGroup 6 (MainChain+Cb) has 1226 elementsGroup 7 ( MainChain+H) has 1230 elementsGroup 8 ( SideChain) has 1232 elementsGroup 9 ( SideChain-H) has 986 elements Group 10 ( Prot-Masses) has 2462 elementsGroup 11 ( Non-Protein) has 23245 elementsGroup 12 ( EST) has 25 elementsGroup 13 ( SOL) has 23220 elementsGroup 14 ( Other) has 23245 elements Select a group: 1Selected 1: 'Protein'Select a group: 12Selected 12: 'EST'Checking for overlap...Calculating hydrogen bonds between two groups of 2462 and 25 atomsFound 349 donors and 692 acceptors in group 'Protein' Found 2 donors and 2 acceptors in group 'EST'Going to allocate 5709 kb of memory, and that's only the beginningtrn version: GMX_trn_file (single precision)Reading frame 0 time 0.000Will do grid-seach on 16x15x14 grid, rcut= 0.35Last frame 100 time 3000.000Found 5 different hydrogen bonds in trajectoryMerging hbonds with Acceptor and Donor swappedReduced number of hbonds from 5 to 5tested 1394 pairsAverage number of hbonds per timeframe 1.218 out of 1041 possibleAny idea? The screen output seems correct to me, but for the fact that it always says no -da option whether I use this option or not, why this?. Thanks for any help. MGiòOn 2/28/06, Anton Feenstra [EMAIL PROTECTED] wrote:MGiò wrote: Thanks, Kia, actually I have used an index.ndx file, but the output is the same. I'll try anyway with the automated procedure by the shell script. Thank you anywayThe script does exactly the same as what you do manually. SO that won'thelp... Can you send the screen output of g_hbond?--Groetjes,Anton* NOTE: New Affiliation, Phone Fax numbers (below) *_ ___ | | ||_ ,| K. Anton Feenstra || / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081A HV Amsterdam - Netherlands|| \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 || | [EMAIL PROTECTED] - www.few.vu.nl/~feenstra/ || | If You See Me Getting High, Knock Me Down (RHCP)||_|___| ___gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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
Re: [gmx-users] Re: g_hbond
MGiò wrote: Well, this was my command line: g_hbond -f ../../traj_c.trr -s ../../topol.tpr -g -num -dist -ang -hbn and this was my screen output No option -da Reading file ../../topol.tpr, VERSION 3.2.1 (single precision) If this was 3.2.1 it's fixed in 3.3 Specify 2 groups to analyze: Opening library file /usr/local/share/gromacs/top/aminoacids.dat Group 0 ( System) has 25707 elements Group 1 ( Protein) has 2462 elements Group 2 ( Protein-H) has 1975 elements Group 3 ( C-alpha) has 247 elements Group 4 (Backbone) has 741 elements Group 5 ( MainChain) has 989 elements Group 6 (MainChain+Cb) has 1226 elements Group 7 ( MainChain+H) has 1230 elements Group 8 ( SideChain) has 1232 elements Group 9 ( SideChain-H) has 986 elements Group10 ( Prot-Masses) has 2462 elements Group11 ( Non-Protein) has 23245 elements Group12 ( EST) has25 elements Group13 ( SOL) has 23220 elements Group14 ( Other) has 23245 elements Select a group: 1 Selected 1: 'Protein' Select a group: 12 Selected 12: 'EST' Checking for overlap... Calculating hydrogen bonds between two groups of 2462 and 25 atoms Found 349 donors and 692 acceptors in group 'Protein' Found 2 donors and 2 acceptors in group 'EST' Going to allocate 5709 kb of memory, and that's only the beginning trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 Will do grid-seach on 16x15x14 grid, rcut= 0.35 Last frame100 time 3000.000 Found 5 different hydrogen bonds in trajectory Merging hbonds with Acceptor and Donor swapped Reduced number of hbonds from 5 to 5 tested 1394 pairs Average number of hbonds per timeframe 1.218 out of 1041 possible Any idea? The screen output seems correct to me, but for the fact that it always says no -da option whether I use this option or not, why this?. Thanks for any help. MGiò On 2/28/06, *Anton Feenstra* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: MGiò wrote: Thanks, Kia, actually I have used an index.ndx file, but the output is the same. I'll try anyway with the automated procedure by the shell script. Thank you anyway The script does exactly the same as what you do manually. SO that won't help... Can you send the screen output of g_hbond? -- Groetjes, Anton * NOTE: New Affiliation, Phone Fax numbers (below) * _ ___ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081A HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 | | | [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] - www.few.vu.nl/~feenstra/ http://www.few.vu.nl/~feenstra/ | | | If You See Me Getting High, Knock Me Down (RHCP)| |_|___| ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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 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
