Re: [gmx-users] How to Calculate tetrahedral order parameter
Den 2019-09-03 kl. 14:02, skrev Soham Sarkar: Sorry, I forgot to mention that I have two systems. One consists of protein-water and the other one consists of protein-water-urea. I need to calculate the tetrahedral order parameter of water around the protein within 0.4nm for these two systems. Sounds like a very difficult problem. I assume you want to evaluate whether the structure is more ordered close to the protein than in bulk. In theory you could find all the water molecules with a radius X from the protein, using gmx trjorder and then generate an index that you pass to gmx hydorder. However if you use a shell of 0.4 nm there will not be enough water to test this, and in addition the water interacting with the protein will not be counted by the program. The most important question you should ask your self is whether you want to get out something that can be measured, in that case you would be better off computing free energies. Thanks and regards- Soham On Tue, 3 Sep 2019, 5:24 pm David van der Spoel, wrote: Den 2019-09-03 kl. 13:26, skrev Soham Sarkar: Dear all, I know this question was asked by many users before but searching them all I did not get how to perform it in GROMACS. Please help me with this. Is there any in built command line exist for Tetrahedral order parameter calculation? If gmx hydorder is the existing tool for calculating tetrahedral order parameter, went through this I did not understand the usage of it too. Thanks in advance- Soham What system, water? -- 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] How to Calculate tetrahedral order parameter
Sorry, I forgot to mention that I have two systems. One consists of protein-water and the other one consists of protein-water-urea. I need to calculate the tetrahedral order parameter of water around the protein within 0.4nm for these two systems. Thanks and regards- Soham On Tue, 3 Sep 2019, 5:24 pm David van der Spoel, wrote: > Den 2019-09-03 kl. 13:26, skrev Soham Sarkar: > > Dear all, > > I know this question was asked by many users before but > searching > > them all I did not get how to perform it in GROMACS. Please help me with > > this. Is there any in built command line exist for Tetrahedral order > > parameter calculation? If gmx hydorder is the existing tool for > calculating > > tetrahedral order parameter, went through this I did not understand the > > usage of it too. > > Thanks in advance- > > Soham > > > What system, water? > > -- > 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] How to Calculate tetrahedral order parameter
Den 2019-09-03 kl. 13:26, skrev Soham Sarkar: Dear all, I know this question was asked by many users before but searching them all I did not get how to perform it in GROMACS. Please help me with this. Is there any in built command line exist for Tetrahedral order parameter calculation? If gmx hydorder is the existing tool for calculating tetrahedral order parameter, went through this I did not understand the usage of it too. Thanks in advance- Soham What system, water? -- 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] How to Calculate tetrahedral order parameter
Dear all, I know this question was asked by many users before but searching them all I did not get how to perform it in GROMACS. Please help me with this. Is there any in built command line exist for Tetrahedral order parameter calculation? If gmx hydorder is the existing tool for calculating tetrahedral order parameter, went through this I did not understand the usage of it too. Thanks in advance- Soham -- 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] How to calculate tetrahedral order parameter in GROMACS
Thanks. I am checking. On Wed, 8 May 2019, 2:30 pm David van der Spoel, wrote: > Den 2019-05-07 kl. 14:34, skrev Soham Sarkar: > > Hello, > >I have two systems. One containing only water and the other one > > contains protein and water. Using g_select I made water in 1st solvation > > shell but the use of g_hydorder I cannot understand. I read the > disscussion > > so far disscussed. For these two systems which index I need to choose, > > water or OW? What is the use of sgang1 and sgang2? Any suggestion > > is appreciated. > > Thanks and regards > > Soham > > > The tool is not made for anything else than water I'm afraid. Please > check this paper for details. > > Bjorn Steen Sæthre, Alex C. Hoffmann and David van der Spoel: Order > parameters and algorithmic approaches for detection and demarcation of > interfaces in hydrate-fluid and ice-fluid systems J. Chem. Theor. > Comput. 10 pp. 5606-5616 (2014) > > -- > 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] How to calculate tetrahedral order parameter in GROMACS
Den 2019-05-07 kl. 14:34, skrev Soham Sarkar: Hello, I have two systems. One containing only water and the other one contains protein and water. Using g_select I made water in 1st solvation shell but the use of g_hydorder I cannot understand. I read the disscussion so far disscussed. For these two systems which index I need to choose, water or OW? What is the use of sgang1 and sgang2? Any suggestion is appreciated. Thanks and regards Soham The tool is not made for anything else than water I'm afraid. Please check this paper for details. Bjorn Steen Sæthre, Alex C. Hoffmann and David van der Spoel: Order parameters and algorithmic approaches for detection and demarcation of interfaces in hydrate-fluid and ice-fluid systems J. Chem. Theor. Comput. 10 pp. 5606-5616 (2014) -- 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] How to calculate tetrahedral order parameter in GROMACS
Hello, I have two systems. One containing only water and the other one contains protein and water. Using g_select I made water in 1st solvation shell but the use of g_hydorder I cannot understand. I read the disscussion so far disscussed. For these two systems which index I need to choose, water or OW? What is the use of sgang1 and sgang2? Any suggestion is appreciated. Thanks and regards Soham -- 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] How to calculate tetrahedral order parameter?
Dear gromacs users, Hello. I am working on bulk water system simulation. I am trying to calculate tetrahedral order parameters in gromacs by using "gmx hydorder" command. Dose anyone know how to process outputs generated by "hydorder" command? It is in the form of output.xpm file. Thanks in advance. -- YK Lee 351-101 Department of physics Institute of natural science Gyeong sang National University -- 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.
