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

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,

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

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

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

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

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

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

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,

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

[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