From: Thomas C. Bishop (bishop_at_latech.edu)
Date: Mon Apr 14 2014 - 08:24:22 CDT
Thanks for directions Axel. After digging into the topotools I used scripting to build all kinds of nanotubes several months ago. but never needed psf for my purposes. The topoTools plugin page has all the info/examples needed. http://www.ks.uiuc.edu/Research/vmd/plugins/topotools/ animate write psf some.psf is listed plain as day.Reminder RTF(ree)M Tom... Axel put it there for a reason!
On Fri, Apr 11, 2014 at 3:44 PM, Thomas C. Bishop <firstname.lastname@example.org> wrote:I believe the scripts and tools that Axlel has for his interactive sims of a nanotube -- bucky ball system might have what you need. in the tar bundle is a parameter file and necessary info for doing the sims w/ lamps and namd BUT I agree w/ Miro I don't actually see how Axel got the psf.... it seems Topo tools were used and the nanotube builder gets you the pdb but where's the psf...the nanobuilder gui says it's going to make one!no it doesn't. the nanotube builder uses the topotools plugin to generate topology data (bonds, angles, dihedrals and impropers) which is then stored in VMD's memory. that is the whole point of most VMD plugins, you use them to either feed VMD data or use the data to do analysis. for writing out, you can just use the regular VMD commands. the GUI can only do so many things. if you want to fully unleash the power of VMD, you *have* to use the script interface. expecting a "just click here" or "do you want this or that" kind of wizard interface is too much effort to write and to inflexible. is it asking too much to expect people to learn a little scripting and programming of crucial tools they are using? anyway, i usually don't have the patience to click through multiple menus to write out files with the GUI and just use animate writeXXX somefile.XXX ... axel.NOTE this particular set of sims is great fun I use it for education/outreach whenever I can. .. SEE Axel;'s movies on youtube https://www.youtube.com/user/templeicms and https://www.youtube.com/watch?v=JGz5oFR71jA Cheers, TOm On 04/11/2014 01:30 PM, Axel Kohlmeyer wrote: On Apr 11, 2014 8:13 PM, "Miro Hodak" <email@example.com> wrote:Maybe this is too obvious, but I do not see it - and I have experience with both NAMD and VMD. I can save coordinates (pdb or other formats) once a nanotube is created, but I see no way of getting a PSF file. I looked into the User's Guide and tried the Automated PSF builder plugin, but I cannot figure this out. If you can be more specific ...Have you tried the script interface?Thanks again, Miro On Fri, Apr 11, 2014 at 1:05 PM, Axel Kohlmeyer <firstname.lastname@example.org> wrote:On Apr 11, 2014 6:56 PM, "Miro Hodak" <email@example.com> wrote:I know of that one, that is how I built my nanotube, but I do not see a way to get a PSF file from this plugin once the nanotube is built.How to save files is explained in the vmd user's guide.Thanks again, Miro On Fri, Apr 11, 2014 at 4:36 AM, Axel Kohlmeyer <firstname.lastname@example.org> wrote:On Thu, Apr 10, 2014 at 7:02 PM, Miro Hodak <email@example.com> wrote:Dear all, I would like to run a NAMD calculation of a nanotube interacting with a protein via non-bonded interactions using CHARMM FF. This looks quite similar to what is done in a tutorial on water flow through nanotubes. However, that tutorial already provides a prebuilt PSF file for the nanotube used there. I want to work with a different nanotube (20,0) and looking at the tutorial and other resources I cannot figure out how to create a PSF file for an arbitrary nanotube I may want to work with. Can anybody help?http://www.ks.uiuc.edu/Research/vmd/plugins/nanotube/Thank you, Miro-- Dr. Axel Kohlmeyer firstname.lastname@example.org http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
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