Re: [gmx-users] Regarding OH, HH vector distribution
Hello Sir, I want to calculate gangle within a cutoff according my rdf. How can I give cutoff in "gmx gangle... " command line. Can anyone help me regarding this? Thank you, On Thu, Aug 1, 2019, 00:52 David van der Spoel wrote: > Den 2019-07-31 kl. 15:00, skrev Omkar Singh: > > I calculated these two vectors with Z-axis now I want to make > > distribution plot p(costheeta) Vs cos(theeta). How can I plot because it > is > > giving the value only theeta. Is there any command. > Try write your own script. > > Thanks > > > > On Wed, Jul 31, 2019, 12:00 David van der Spoel > > wrote: > > > >> Den 2019-07-31 kl. 06:12, skrev Omkar Singh: > >>> Thanks Sir, > >>> I did like that only, Now how can I make the distribution plot for > these > >>> vectors. Eventhough I used "gmx analyze -f .xvg -dist .." command. > >> But > >>> results is not proper. Can you suggest me regarding this? > >>> Thank you > >>> > >> How about gmx gangle -oh ? > >> > >>> > >>> On Tue, Jul 30, 2019, 17:27 David van der Spoel > >>> wrote: > >>> > Den 2019-07-30 kl. 07:55, skrev Omkar Singh: > > Hi, > > I did by "gmx gangle ..." command. But I am not getting good result, > > because I have a doubt in ndx file. Can you help me for making ndx > file. > > How should I select the atom for vectors. > For OH it should be > 1 2 > 1 3 > 4 5 > 4 6 > 7 8 > 7 9 > etc., assuming a three particle water model with atoms O H H. > For HH it should be > 2 3 > 5 6 > 8 9 > etc. > A simple script would do it. The dipole vector is somewhat harder. > > Thanks > > > > On Mon, Jul 29, 2019, 22:50 David van der Spoel < > sp...@xray.bmc.uu.se> > > wrote: > > > >> Den 2019-07-29 kl. 18:26, skrev Omkar Singh: > >>> Hi, > >>> Meaning is that If I want to calculate angle between OH, HH and dip > >> vector > >>> with positive Z-axis. How can I make index file for this issue? And > >> is > it > >>> possible that the angle distribution of these vectors for bulk > water > >>> aproximatly linear. Hope now question is clear. > >> Probably. Check gmx gangle -g2 z > >>> > >>> Thanks > >>> > >>> On Mon, Jul 29, 2019, 16:33 David van der Spoel < > >> sp...@xray.bmc.uu.se> > >>> wrote: > >>> > Den 2019-07-29 kl. 12:24, skrev Omkar Singh: > > Hello everyone, > > Is it possible that the probability distribution of HH, OH vector > >> for > bulk > > water is approximately linear? > > > What do you mean? > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > >> or > send a mail to gmx-users-requ...@gromacs.org. > > >> > >> > >> -- > >> David van der Spoel, Ph.D., Professor of Biology > >> Head of Department, Cell & Molecular Biology, Uppsala University. > >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > >> http://www.icm.uu.se > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > >> > >> > >> -- > >> David van der Spoel, Ph.D., Professor of Biology > >> Head of Department, Cell & Molecular Biology, Uppsala University. > >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
Re: [gmx-users] Regarding OH, HH vector distribution
Den 2019-07-31 kl. 15:00, skrev Omkar Singh: I calculated these two vectors with Z-axis now I want to make distribution plot p(costheeta) Vs cos(theeta). How can I plot because it is giving the value only theeta. Is there any command. Try write your own script. Thanks On Wed, Jul 31, 2019, 12:00 David van der Spoel wrote: Den 2019-07-31 kl. 06:12, skrev Omkar Singh: Thanks Sir, I did like that only, Now how can I make the distribution plot for these vectors. Eventhough I used "gmx analyze -f .xvg -dist .." command. But results is not proper. Can you suggest me regarding this? Thank you How about gmx gangle -oh ? On Tue, Jul 30, 2019, 17:27 David van der Spoel wrote: Den 2019-07-30 kl. 07:55, skrev Omkar Singh: Hi, I did by "gmx gangle ..." command. But I am not getting good result, because I have a doubt in ndx file. Can you help me for making ndx file. How should I select the atom for vectors. For OH it should be 1 2 1 3 4 5 4 6 7 8 7 9 etc., assuming a three particle water model with atoms O H H. For HH it should be 2 3 5 6 8 9 etc. A simple script would do it. The dipole vector is somewhat harder. Thanks On Mon, Jul 29, 2019, 22:50 David van der Spoel wrote: Den 2019-07-29 kl. 18:26, skrev Omkar Singh: Hi, Meaning is that If I want to calculate angle between OH, HH and dip vector with positive Z-axis. How can I make index file for this issue? And is it possible that the angle distribution of these vectors for bulk water aproximatly linear. Hope now question is clear. Probably. Check gmx gangle -g2 z Thanks On Mon, Jul 29, 2019, 16:33 David van der Spoel < sp...@xray.bmc.uu.se> wrote: Den 2019-07-29 kl. 12:24, skrev Omkar Singh: Hello everyone, Is it possible that the probability distribution of HH, OH vector for bulk water is approximately linear? What do you mean? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding OH, HH vector distribution
I calculated these two vectors with Z-axis now I want to make distribution plot p(costheeta) Vs cos(theeta). How can I plot because it is giving the value only theeta. Is there any command. Thanks On Wed, Jul 31, 2019, 12:00 David van der Spoel wrote: > Den 2019-07-31 kl. 06:12, skrev Omkar Singh: > > Thanks Sir, > > I did like that only, Now how can I make the distribution plot for these > > vectors. Eventhough I used "gmx analyze -f .xvg -dist .." command. > But > > results is not proper. Can you suggest me regarding this? > > Thank you > > > How about gmx gangle -oh ? > > > > > On Tue, Jul 30, 2019, 17:27 David van der Spoel > > wrote: > > > >> Den 2019-07-30 kl. 07:55, skrev Omkar Singh: > >>> Hi, > >>> I did by "gmx gangle ..." command. But I am not getting good result, > >>> because I have a doubt in ndx file. Can you help me for making ndx > >> file. > >>> How should I select the atom for vectors. > >> For OH it should be > >> 1 2 > >> 1 3 > >> 4 5 > >> 4 6 > >> 7 8 > >> 7 9 > >> etc., assuming a three particle water model with atoms O H H. > >> For HH it should be > >> 2 3 > >> 5 6 > >> 8 9 > >> etc. > >> A simple script would do it. The dipole vector is somewhat harder. > >>> Thanks > >>> > >>> On Mon, Jul 29, 2019, 22:50 David van der Spoel > >>> wrote: > >>> > Den 2019-07-29 kl. 18:26, skrev Omkar Singh: > > Hi, > > Meaning is that If I want to calculate angle between OH, HH and dip > vector > > with positive Z-axis. How can I make index file for this issue? And > is > >> it > > possible that the angle distribution of these vectors for bulk water > > aproximatly linear. Hope now question is clear. > Probably. Check gmx gangle -g2 z > > > > Thanks > > > > On Mon, Jul 29, 2019, 16:33 David van der Spoel < > sp...@xray.bmc.uu.se> > > wrote: > > > >> Den 2019-07-29 kl. 12:24, skrev Omkar Singh: > >>> Hello everyone, > >>> Is it possible that the probability distribution of HH, OH vector > for > >> bulk > >>> water is approximately linear? > >>> > >> What do you mean? > >> > >> -- > >> David van der Spoel, Ph.D., Professor of Biology > >> Head of Department, Cell & Molecular Biology, Uppsala University. > >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > >> http://www.icm.uu.se > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > >> > >> > >> -- > >> David van der Spoel, Ph.D., Professor of Biology > >> Head of Department, Cell & Molecular Biology, Uppsala University. > >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > >> http://www.icm.uu.se > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit
Re: [gmx-users] Regarding OH, HH vector distribution
Den 2019-07-31 kl. 06:12, skrev Omkar Singh: Thanks Sir, I did like that only, Now how can I make the distribution plot for these vectors. Eventhough I used "gmx analyze -f .xvg -dist .." command. But results is not proper. Can you suggest me regarding this? Thank you How about gmx gangle -oh ? On Tue, Jul 30, 2019, 17:27 David van der Spoel wrote: Den 2019-07-30 kl. 07:55, skrev Omkar Singh: Hi, I did by "gmx gangle ..." command. But I am not getting good result, because I have a doubt in ndx file. Can you help me for making ndx file. How should I select the atom for vectors. For OH it should be 1 2 1 3 4 5 4 6 7 8 7 9 etc., assuming a three particle water model with atoms O H H. For HH it should be 2 3 5 6 8 9 etc. A simple script would do it. The dipole vector is somewhat harder. Thanks On Mon, Jul 29, 2019, 22:50 David van der Spoel wrote: Den 2019-07-29 kl. 18:26, skrev Omkar Singh: Hi, Meaning is that If I want to calculate angle between OH, HH and dip vector with positive Z-axis. How can I make index file for this issue? And is it possible that the angle distribution of these vectors for bulk water aproximatly linear. Hope now question is clear. Probably. Check gmx gangle -g2 z Thanks On Mon, Jul 29, 2019, 16:33 David van der Spoel wrote: Den 2019-07-29 kl. 12:24, skrev Omkar Singh: Hello everyone, Is it possible that the probability distribution of HH, OH vector for bulk water is approximately linear? What do you mean? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding OH, HH vector distribution
Thanks Sir, I did like that only, Now how can I make the distribution plot for these vectors. Eventhough I used "gmx analyze -f .xvg -dist .." command. But results is not proper. Can you suggest me regarding this? Thank you On Tue, Jul 30, 2019, 17:27 David van der Spoel wrote: > Den 2019-07-30 kl. 07:55, skrev Omkar Singh: > > Hi, > > I did by "gmx gangle ..." command. But I am not getting good result, > > because I have a doubt in ndx file. Can you help me for making ndx > file. > > How should I select the atom for vectors. > For OH it should be > 1 2 > 1 3 > 4 5 > 4 6 > 7 8 > 7 9 > etc., assuming a three particle water model with atoms O H H. > For HH it should be > 2 3 > 5 6 > 8 9 > etc. > A simple script would do it. The dipole vector is somewhat harder. > > Thanks > > > > On Mon, Jul 29, 2019, 22:50 David van der Spoel > > wrote: > > > >> Den 2019-07-29 kl. 18:26, skrev Omkar Singh: > >>> Hi, > >>> Meaning is that If I want to calculate angle between OH, HH and dip > >> vector > >>> with positive Z-axis. How can I make index file for this issue? And is > it > >>> possible that the angle distribution of these vectors for bulk water > >>> aproximatly linear. Hope now question is clear. > >> Probably. Check gmx gangle -g2 z > >>> > >>> Thanks > >>> > >>> On Mon, Jul 29, 2019, 16:33 David van der Spoel > >>> wrote: > >>> > Den 2019-07-29 kl. 12:24, skrev Omkar Singh: > > Hello everyone, > > Is it possible that the probability distribution of HH, OH vector for > bulk > > water is approximately linear? > > > What do you mean? > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > >> > >> > >> -- > >> David van der Spoel, Ph.D., Professor of Biology > >> Head of Department, Cell & Molecular Biology, Uppsala University. > >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > >> http://www.icm.uu.se > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding OH, HH vector distribution
Den 2019-07-30 kl. 07:55, skrev Omkar Singh: Hi, I did by "gmx gangle ..." command. But I am not getting good result, because I have a doubt in ndx file. Can you help me for making ndx file. How should I select the atom for vectors. For OH it should be 1 2 1 3 4 5 4 6 7 8 7 9 etc., assuming a three particle water model with atoms O H H. For HH it should be 2 3 5 6 8 9 etc. A simple script would do it. The dipole vector is somewhat harder. Thanks On Mon, Jul 29, 2019, 22:50 David van der Spoel wrote: Den 2019-07-29 kl. 18:26, skrev Omkar Singh: Hi, Meaning is that If I want to calculate angle between OH, HH and dip vector with positive Z-axis. How can I make index file for this issue? And is it possible that the angle distribution of these vectors for bulk water aproximatly linear. Hope now question is clear. Probably. Check gmx gangle -g2 z Thanks On Mon, Jul 29, 2019, 16:33 David van der Spoel wrote: Den 2019-07-29 kl. 12:24, skrev Omkar Singh: Hello everyone, Is it possible that the probability distribution of HH, OH vector for bulk water is approximately linear? What do you mean? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding OH, HH vector distribution
Hi, I did by "gmx gangle ..." command. But I am not getting good result, because I have a doubt in ndx file. Can you help me for making ndx file. How should I select the atom for vectors. Thanks On Mon, Jul 29, 2019, 22:50 David van der Spoel wrote: > Den 2019-07-29 kl. 18:26, skrev Omkar Singh: > > Hi, > > Meaning is that If I want to calculate angle between OH, HH and dip > vector > > with positive Z-axis. How can I make index file for this issue? And is it > > possible that the angle distribution of these vectors for bulk water > > aproximatly linear. Hope now question is clear. > Probably. Check gmx gangle -g2 z > > > > Thanks > > > > On Mon, Jul 29, 2019, 16:33 David van der Spoel > > wrote: > > > >> Den 2019-07-29 kl. 12:24, skrev Omkar Singh: > >>> Hello everyone, > >>> Is it possible that the probability distribution of HH, OH vector for > >> bulk > >>> water is approximately linear? > >>> > >> What do you mean? > >> > >> -- > >> David van der Spoel, Ph.D., Professor of Biology > >> Head of Department, Cell & Molecular Biology, Uppsala University. > >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > >> http://www.icm.uu.se > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding OH, HH vector distribution
Den 2019-07-29 kl. 18:26, skrev Omkar Singh: Hi, Meaning is that If I want to calculate angle between OH, HH and dip vector with positive Z-axis. How can I make index file for this issue? And is it possible that the angle distribution of these vectors for bulk water aproximatly linear. Hope now question is clear. Probably. Check gmx gangle -g2 z Thanks On Mon, Jul 29, 2019, 16:33 David van der Spoel wrote: Den 2019-07-29 kl. 12:24, skrev Omkar Singh: Hello everyone, Is it possible that the probability distribution of HH, OH vector for bulk water is approximately linear? What do you mean? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding OH, HH vector distribution
Hi, Meaning is that If I want to calculate angle between OH, HH and dip vector with positive Z-axis. How can I make index file for this issue? And is it possible that the angle distribution of these vectors for bulk water aproximatly linear. Hope now question is clear. Thanks On Mon, Jul 29, 2019, 16:33 David van der Spoel wrote: > Den 2019-07-29 kl. 12:24, skrev Omkar Singh: > > Hello everyone, > > Is it possible that the probability distribution of HH, OH vector for > bulk > > water is approximately linear? > > > What do you mean? > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding OH, HH vector distribution
Den 2019-07-29 kl. 12:24, skrev Omkar Singh: Hello everyone, Is it possible that the probability distribution of HH, OH vector for bulk water is approximately linear? What do you mean? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Regarding OH, HH vector distribution
Hello everyone, Is it possible that the probability distribution of HH, OH vector for bulk water is approximately linear? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
