Re: [gmx-users] g_hbond and 4.5.2 version
Dear Justin, maybe following information helps you. When I evaluated the number of hydrogen bonds between two different groups, particularly, water and frozen atoms of the siloxane surface I got the same results with both version of GROMACS, 4.0.3 and 4.5.2.GreetingsZuzanaOn 02/15/11, Zuzana Benkova zuzana.benk...@savba.sk wrote:Hello Justin, I was using cubic boxes. GreetingsZuzanaOn 02/15/11, Erik Marklund er...@xray.bmc.uu.se wrote:Justin A. Lemkul skrev 2011-02-09 23.03:Zuzana Benkova wrote:Dear GROMACS users,I have used g_hbond of version 4.5.2 to analyze number of hydrogen bonds in water. I got the average number per time frame and number of water oxygen atoms equal to 0.839. When I used g_hbond of version 4.0.7 I got 1.677, which is twice the former value. TIP3P model predicts over 3 hydrogen bonds per one water molecule. I am a bit puzzled. If I multiply the digit from version 4.0.7. by 2 I get the expected number. That is why I supposed that the number of 1.677 means per one water oxygen and per one water molecule means 2x1.677 since two water molecules participate at one hydrogen bond.However, I do not know yet if my interpretation is correct and how to interpret the number obtained by version 4.5.2.I would appreciate any help. Thank you in advance.Try pulling the latest stable development version. This issue was reported in 4.5.1:http://lists.gromacs.org/pipermail/gmx-users/2010-October/054905.htmlbut not fixed until after 4.5.3 was released:http://lists.gromacs.org/pipermail/gmx-users/2010-December/056406.html-JustinGreetingsZuzanaAre people who are reporting this error using a triclinic boxes or cuboid boxes. That information may help my bugfixing.-- ---Erik Marklund, PhD studentDept. of Cell and Molecular Biology, Uppsala University.Husargatan 3, Box 596, 75124 Uppsala, Swedenphone: +46 18 471 4537 fax: +46 18 511 755er...@xray.bmc.uu.se http://folding.bmc.uu.se/-- gmx-users mailing list gmx-users@gromacs.orghttp://lists.gromacs.org/mailman/listinfo/gmx-usersPlease 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] g_hbond and 4.5.2 version
Hi, That suggets it's related to the new merge-on-the-fly-code and not the pbc handling. And it's me, not Justin, who's fixing and probably creating the bugs. :-) Cheers, Erik Zuzana Benkova skrev 2011-02-16 19.58: Dear Justin, maybe following information helps you. When I evaluated the number of hydrogen bonds between two different groups, particularly, water and frozen atoms of the siloxane surface I got the same results with both version of GROMACS, 4.0.3 and 4.5.2. Greetings Zuzana On 02/15/11, *Zuzana Benkova * zuzana.benk...@savba.sk wrote: Hello Justin, I was using cubic boxes. Greetings Zuzana On 02/15/11, *Erik Marklund * er...@xray.bmc.uu.se wrote: Justin A. Lemkul skrev 2011-02-09 23.03: Zuzana Benkova wrote: Dear GROMACS users, I have used g_hbond of version 4.5.2 to analyze number of hydrogen bonds in water. I got the average number per time frame and number of water oxygen atoms equal to 0.839. When I used g_hbond of version 4.0.7 I got 1.677, which is twice the former value. TIP3P model predicts over 3 hydrogen bonds per one water molecule. I am a bit puzzled. If I multiply the digit from version 4.0.7. by 2 I get the expected number. That is why I supposed that the number of 1.677 means per one water oxygen and per one water molecule means 2x1.677 since two water molecules participate at one hydrogen bond. However, I do not know yet if my interpretation is correct and how to interpret the number obtained by version 4.5.2. I would appreciate any help. Thank you in advance. Try pulling the latest stable development version. This issue was reported in 4.5.1: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054905.html but not fixed until after 4.5.3 was released: http://lists.gromacs.org/pipermail/gmx-users/2010-December/056406.html -Justin Greetings Zuzana Are people who are reporting this error using a triclinic boxes or cuboid boxes. That information may help my bugfixing. -- --- 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/ -- 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 -- --- 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] g_hbond and 4.5.2 version
Justin A. Lemkul skrev 2011-02-09 23.03: Zuzana Benkova wrote: Dear GROMACS users, I have used g_hbond of version 4.5.2 to analyze number of hydrogen bonds in water. I got the average number per time frame and number of water oxygen atoms equal to 0.839. When I used g_hbond of version 4.0.7 I got 1.677, which is twice the former value. TIP3P model predicts over 3 hydrogen bonds per one water molecule. I am a bit puzzled. If I multiply the digit from version 4.0.7. by 2 I get the expected number. That is why I supposed that the number of 1.677 means per one water oxygen and per one water molecule means 2x1.677 since two water molecules participate at one hydrogen bond. However, I do not know yet if my interpretation is correct and how to interpret the number obtained by version 4.5.2. I would appreciate any help. Thank you in advance. Try pulling the latest stable development version. This issue was reported in 4.5.1: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054905.html but not fixed until after 4.5.3 was released: http://lists.gromacs.org/pipermail/gmx-users/2010-December/056406.html -Justin Greetings Zuzana Are people who are reporting this error using a triclinic boxes or cuboid boxes. That information may help my bugfixing. -- --- 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] g_hbond and 4.5.2 version
Hello Justin, I was using cubic boxes. GreetingsZuzanaOn 02/15/11, Erik Marklund er...@xray.bmc.uu.se wrote:Justin A. Lemkul skrev 2011-02-09 23.03:Zuzana Benkova wrote:Dear GROMACS users,I have used g_hbond of version 4.5.2 to analyze number of hydrogen bonds in water. I got the average number per time frame and number of water oxygen atoms equal to 0.839. When I used g_hbond of version 4.0.7 I got 1.677, which is twice the former value. TIP3P model predicts over 3 hydrogen bonds per one water molecule. I am a bit puzzled. If I multiply the digit from version 4.0.7. by 2 I get the expected number. That is why I supposed that the number of 1.677 means per one water oxygen and per one water molecule means 2x1.677 since two water molecules participate at one hydrogen bond.However, I do not know yet if my interpretation is correct and how to interpret the number obtained by version 4.5.2.I would appreciate any help. Thank you in advance.Try pulling the latest stable development version. This issue was reported in 4.5.1:http://lists.gromacs.org/pipermail/gmx-users/2010-October/054905.htmlbut not fixed until after 4.5.3 was released:http://lists.gromacs.org/pipermail/gmx-users/2010-December/056406.html-JustinGreetingsZuzanaAre people who are reporting this error using a triclinic boxes or cuboid boxes. That information may help my bugfixing.-- ---Erik Marklund, PhD studentDept. of Cell and Molecular Biology, Uppsala University.Husargatan 3, Box 596, 75124 Uppsala, Swedenphone: +46 18 471 4537 fax: +46 18 511 755er...@xray.bmc.uu.se http://folding.bmc.uu.se/-- gmx-users mailing list gmx-users@gromacs.orghttp://lists.gromacs.org/mailman/listinfo/gmx-usersPlease 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] g_hbond and 4.5.2 version
Dear GROMACS users,I have used g_hbond of version 4.5.2 to analyze number of hydrogen bonds in water. I got the average number per time frame and number of water oxygen atoms equal to 0.839. When I used g_hbond of version 4.0.7 I got 1.677, which is twice the former value. TIP3P model predicts over 3 hydrogen bonds per one water molecule. I am a bit puzzled. If I multiply the digit from version 4.0.7. by 2 I get the expected number. That is why I supposed that the number of 1.677 means per one water oxygen and per one water molecule means 2x1.677 since two water molecules participate at one hydrogen bond. However, I do not know yet if my interpretation is correct and how to interpret the number obtained by version 4.5.2. I would appreciate any help. Thank you in advance.GreetingsZuzana -- 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 and 4.5.2 version
Zuzana Benkova wrote: Dear GROMACS users, I have used g_hbond of version 4.5.2 to analyze number of hydrogen bonds in water. I got the average number per time frame and number of water oxygen atoms equal to 0.839. When I used g_hbond of version 4.0.7 I got 1.677, which is twice the former value. TIP3P model predicts over 3 hydrogen bonds per one water molecule. I am a bit puzzled. If I multiply the digit from version 4.0.7. by 2 I get the expected number. That is why I supposed that the number of 1.677 means per one water oxygen and per one water molecule means 2x1.677 since two water molecules participate at one hydrogen bond. However, I do not know yet if my interpretation is correct and how to interpret the number obtained by version 4.5.2. I would appreciate any help. Thank you in advance. Try pulling the latest stable development version. This issue was reported in 4.5.1: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054905.html but not fixed until after 4.5.3 was released: http://lists.gromacs.org/pipermail/gmx-users/2010-December/056406.html -Justin Greetings Zuzana -- 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
