Re: [gmx-users] Membrane simulation with OPLS ff.
On 26 Sep, 2013, at 19:50, Justin Lemkul wrote: > On 9/26/13 10:47 PM, Christopher Neale wrote: >> Dear Karthi: >> >> As far as I am aware, there is no OPLSAA lipid force field. I have used >> Berger lipids with OPLSAA protein >> ( http://www.pomeslab.com/files/lipidCombinationRules.pdf ) but that is >> mixing a UA lipid with an AA protein >> so be aware of possible problems arising out of that. >> > > There are OPLS-compatible lipids, though they are UA, but specifically > designed to be used with OPLS-AA: > > dx.doi.org/10.1021/ct900086b > > I have not seen these parameters used very widely, though. I have used the "Ulmschneider lipids" quite a bit and they are working well for me. You can obtain them from Lipidbook, http://lipidbook.bioch.ox.ac.uk/ , in the browser http://lipidbook.bioch.ox.ac.uk/package/ select OPLS and Gromacs. Specifically, POPC is http://lipidbook.bioch.ox.ac.uk/package/show/id/52.html Oliver -- Oliver Beckstein * oliver.beckst...@asu.edu http://becksteinlab.physics.asu.edu/ Arizona State University Department of Physics Tempe, AZ 85287-1504 USA Office: PSF 348 Phone: +1 (480) 727-9765 FAX: +1 (480) 965-4669 Department of Physics: http://physics.asu.edu/home/people/faculty/oliver-beckstein Center for Biological Physics: http://biophysics.asu.edu/CBP/person.php?ID=343 -- 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] fraction of native contacts calculation
>>> Is there any way to calculate fraction of native contacts during the >>> simulation in gromacs. I searched the archives but didn't found any >>> significant clue. >> >> At present, there is no way to do this. Likely one could modify the >> g_mindist code to do this - it would be a very nice feature. >> > > If one could get the -sel option of g_hbond to work again then you would get > such information with -contact. > In the meantime you might be able to use MDAnalysis http://mdanalysis.googlecode.com/ and the native contact analysis in MDAnalysis.analysis.contacts, see http://packages.python.org/MDAnalysis/documentation_pages/analysis/contacts.html (If you have questions about MDAnalysis then please ask them on that project's discussion group http://groups.google.com/group/mdnalysis-discussion — people there are more than happy to help.) Best wishes, Oliver -- Oliver Beckstein * oliver.beckst...@asu.edu http://becksteinlab.physics.asu.edu/ Arizona State University Department of Physics Tempe, AZ 85287-1504 USA Office: PSF 348 Phone: +1 (480) 727-9765 FAX: +1 (480) 965-4669 Department of Physics: http://physics.asu.edu/home/people/faculty/oliver-beckstein Center for Biological Physics: http://biophysics.asu.edu/CBP/person.php?ID=343 -- 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] Obtain the flux of water
On 31 Dec, 2011, at 21:50, Saeid Akbarshahi wrote: > Whether there is a program in Gromacs that would directly or indirectly > obtained the flux of water ? > > How to obtain the flux water in Gromacs ? A (long) while back I wrote g_count and g_flux, which are primarily useful for looking at flux through pores and channels. https://github.com/orbeckst/g_count However, the code probably needs to be updated to properly work with the latest Gromacs releases. If you use it then please check carefully that the results are what you expect them to be (e.g. based on visual inspection). Feel free to report problems and fixes/patches through the Issue tracker https://github.com/orbeckst/g_count/issues . Cheers, Oliver -- Oliver Beckstein * oliver.beckst...@asu.edu http://physics.asu.edu/home/people/faculty/oliver-beckstein Arizona State University Department of Physics Tempe, AZ 85287-1504 USA -- 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] force field parameters for lipids on lipidbook.bioch.ox.ac.uk
Hi, readers of this list who are interested in the simulation of membranes, membrane proteins, micelles etc. might be interested in a new web site we recently set up [1]: http://lipidbook.bioch.ox.ac.uk It is a public repository for force field parameters with a special emphasis on lipids, detergents, and similar molecules that are of interest when simulating biological membranes. It acts as a warehouse for parameter files that are supplied by the community. Anyone can * browse and download parameters; * deposit their own parameters; and * comment on parameter sets. We invite you to try it out and especially to consider uploading your own published parametrizations to the site: They are linked to the citation and users get the parameters together with a text file reminding them to cite YOU. If you can't find what you are looking for on Lipidbook you might want to have a look at some other sites such as the ones in the (probably incomplete) list at http://lipidbook.bioch.ox.ac.uk/package/resources.html PLEASE do not report problems or questions about Lipidbook to the mailing list (people might get annoyed) but rather contact someone listed under http://lipidbook.bioch.ox.ac.uk/package/about.html#contact or file a problem with the Lipidbook Issue Tracker http://lipidbook.bioch.ox.ac.uk/trac/ . Many thanks for your time! Oliver Beckstein Jan Domanski Phill Stansfeld Mark Sansom [1] J. Domański, P. Stansfeld, M.S.P. Sansom, and O. Beckstein. Lipidbook: A Public Repository for Force Field Parameters Used in Membrane Simulations. J. Membrane Biol. 236 (2010), 255—258. http://dx.doi.org/10.1007/s00232-010-9296-8 -- Oliver Beckstein SBCB Unit, University of Oxford email: oliver.beckst...@bioch.ox.ac.uk web: http://sbcb.bioch.ox.ac.uk/oliver/ -- 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
