[gmx-users] How to modify the code g_hbond to analyze the non-traditional hydrogen bonds like C-H...O
Dear gmxers, I want to analyze the non-traditional hydrogen bonds like C-H...O. To my best knowledge, the g_hbond code can be used for traditional hydrogen bonds but not for our case. One possible solution is to modify the g_hbond code to include the non-traditional hydrogen bonds. However, the code is too long and too complex to understand for me, a non-programmer. Could you give me hints to cope with this, please? Thank you very much for any replies! Yours sincerely, Chaofu Wu -- 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] How to modify the code g_hbond to analyze the non-traditional hydrogen bonds like C-H...O
On 2013-06-30 11:34, Wu Chaofu wrote: Dear gmxers, I want to analyze the non-traditional hydrogen bonds like C-H...O. To my best knowledge, the g_hbond code can be used for traditional hydrogen bonds but not for our case. One possible solution is to modify the g_hbond code to include the non-traditional hydrogen bonds. However, the code is too long and too complex to understand for me, a non-programmer. Could you give me hints to cope with this, please? Thank you very much for any replies! Yours sincerely, Chaofu Wu g_hbond will be rewritten from scratch more or less for 5.0 therefore I would like to try to discourage modifications. That said, a small hack in search_donors() should do the trick. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Re: Pulling
If you use periodic boundary conditions, there is no need that the protein stays at one side of the box. For the pulling simulation: Read the chapters 6.4 (explains the pull-code) and 7.3.21 (explains the mdp-paramters). Additional information you an also get from Justin Tutorial for Umbrella Sampling (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/). Greetings Thomas Am 30.06.2013 01:07, schrieb gmx-users-requ...@gromacs.org: Dear users, I have a sytem including protein, lipids, and water. My protein is in center of the box. Now i want it stays at one side of the box. Which tool or command should i use to pull the protein to a any mong mu???n location ? Thankful for any help ! Thu -- 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] unit conversion
Hi, When I convert FF parameters from OPLS (in Gromacs) to Charmm, I divide bond and angle force constants, i.e., Kb and Ktheta, by 836.8 and 8.368. However, parameters for tip3p water do not convert properly in this ways. For example, Kb = 502416.0 kJ/mol/nm^2 for OW-HW in Gromacs and 450.0 kcal/mol/A^2 in Charmm. 502416.0/836.8 = 600.4 instead of 450.0. I wonder what I did is incorrect. Thanks. Hyunjin. -- 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] unit conversion
On 6/30/13 12:11 PM, Hyunjin Kim wrote: Hi, When I convert FF parameters from OPLS (in Gromacs) to Charmm, I divide bond and angle force constants, i.e., Kb and Ktheta, by 836.8 and 8.368. However, parameters for tip3p water do not convert properly in this ways. For example, Kb = 502416.0 kJ/mol/nm^2 for OW-HW in Gromacs and 450.0 kcal/mol/A^2 in Charmm. 502416.0/836.8 = 600.4 instead of 450.0. I wonder what I did is incorrect. CHARMM has its own special variation of TIP3P that corresponds to the values you are trying to produce. In tip3.itp, it's the #ifdef CHARMM_TIP3P block. The other parameters are for standard TIP3P. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Covariance file format
Hi Ankita, The fie contains the eigenvectors as x1 y1 z1 x2 y2 z2 ... xN yN zN Hope it helps, Tsjerk On Mon, Jul 1, 2013 at 1:38 AM, Ankita naithani ankitanaith...@gmail.comwrote: Hi, I wanted to know the exact format of covariance.dat file as generated by g_covar during covariance analysis. The file format mentioned in the manual was not quite clear to understand. I need to use the matrix information n so needed to know how the data is stored. My matrix is for 1992 calpha atoms. It would be really helpful if someone could explain the file format. Kind regards, Ankita -- Ankita Naithani -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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
