Thanks for the reply. In fact I had the trajectory with water but then I removed it to have smaller size of files. the point is that It didn't complain or crash when I was using that trajectory, choosing water in the groups selecting. but it didn't also generate any output. that is why I asked that ...
Anyway since I have gro files time to time, I think I will cat all the gro file and use that for analysis of h_bond. Fahimeh --- On Fri, 9/17/10, David van der Spoel <sp...@xray.bmc.uu.se> wrote: From: David van der Spoel <sp...@xray.bmc.uu.se> Subject: Re: [gmx-users] g_hbond To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Date: Friday, September 17, 2010, 9:37 PM On 9/17/10 5:37 PM, Justin A. Lemkul wrote: > > > Fahimeh Baftizadeh Baghal wrote: >> hello, >> I have a trajectory generated by gromacs in which I excluded water and >> there is only protein, now I like to see how does the number of h_bond >> between water and protein change during the trajectory. In fact when I >> use g_hbond I can choose the water and protein but I was wondering >> where does the information about water come from?? > > Certainly you can choose whatever groups are present (either from > default groups or from those in an index file), but I would imagine the > command will either fail or simply identify that there are no hydrogen > bond donors or acceptors within what would otherwise be water. > > If you have not saved the coordinates for water, you cannot run any > command to analyze properties related to or involving water. In theory you could get an approximate number from analyzing what polar groups are not hydrogen bonded intramolecularly. There is not ready tool to do this. The quickest solution is probably to rerun the simulation. In most cases human time is more valuable than computer time. > > -Justin > >> thank you in advance for your time >> >> Fahimeh > -- David. ________________________________________________________________________ David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -- gmx-users mailing list gmx-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
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