Re: [gmx-users] calculation of the order parameter S2
On Sun, 04 Jan 2009 13:38:33 +1100 Mark Abraham wrote: Dechang Li wrote: Dear all, I want to use g_rotacf to calculate the order parameter(S2, N-H bond in main chian). The tool g_rotacf needs an index.ndx file that contains two vectors. g_rotacf wants the index number of two atoms to calculate the order parameter of an NH vector. You should give the index number of the atoms N and H and use the option -d. Note that you have to take care of the overall rotation of the molecule in the calculation. Either you remove it before the calculation or you include it in the fit of the correlation function. How can I make the index.ndx file? Can I use the tool make_ndx to do this? Or I need to write the file manually? See http://wiki.gromacs.org/index.php/Index_File. I think you just want to write a file by hand. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php - XAvier Periole - PhD - Molecular Dynamics Group - Computation and NMR University of Groningen The Netherlands - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Generalized Born
> Not yet, but in 4.1 it will. The strange thing is that it "works" in the sense that implicit_solvent = GBSA does not crash :) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] problem with mdrun in parallel
huifang liu wrote: Hello, everybody, I recently installed FFTW-3.0.1, mpich-1.2.7 and Gromacs 3.3.3 on my workstation with two 8-cords CPUs. I think i installed them correctly, beause it runs normally with other parellel MD software. It also went nomorally when i run mdrun command in gromacs with 4 nodes. The problem is it doesn't run with when it is up to 8 nodes. In fact, i only change the '-np 4' to '-np 8' in both grompp and mdrun commmand. When i typed the 'top' command, it shows there are only two node are running. And after a little while, it stopped run with the follow error: p7_19858: p4_error: Timeout in establishing connection to remote process: 0 p5_19808: p4_error: Timeout in establishing connection to remote process: 0 p6_19832: p4_error: Timeout in establishing connection to remote process: 0 p0_19710: (324.359375) net_recv failed for fd = 9 p0_19710: p4_error: net_recv read, errno = : 104 In addition, it runs very well, when i use '-np 5' So how is your MPI environment configured? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] problem with mdrun in parallel
Hello, everybody, I recently installed FFTW-3.0.1, mpich-1.2.7 and Gromacs 3.3.3 on my workstation with two 8-cords CPUs. I think i installed them correctly, beause it runs normally with other parellel MD software. It also went nomorally when i run mdrun command in gromacs with 4 nodes. The problem is it doesn't run with when it is up to 8 nodes. In fact, i only change the '-np 4' to '-np 8' in both grompp and mdrun commmand. When i typed the 'top' command, it shows there are only two node are running. And after a little while, it stopped run with the follow error: p7_19858: p4_error: Timeout in establishing connection to remote process: 0 p5_19808: p4_error: Timeout in establishing connection to remote process: 0 p6_19832: p4_error: Timeout in establishing connection to remote process: 0 p0_19710: (324.359375) net_recv failed for fd = 9 p0_19710: p4_error: net_recv read, errno = : 104 In addition, it runs very well, when i use '-np 5' Hope for your help. Thanks Huifang -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) Shanghai, China, 200032 Cell phone: +86-13764669357 E-mail: huifangliu1...@gmail.com Fax: (86-21)54237264 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Generalized Born
Semen Esilevsky wrote: Dear All, I've just found that the implicit solvent code seems to work in Gromacs 4.x, the feature I was waiting for a long time to play with. However, there is absolutely no documentation - not a single word anywhere except the traceback of GB options in mdout.mdp (that is how I found this out). Is this feature still experimental? Where can I read about the method implemented? Not yet, but in 4.1 it will. Thanks in advance! Semen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Generalized Born
Dear All, I've just found that the implicit solvent code seems to work in Gromacs 4.x, the feature I was waiting for a long time to play with. However, there is absolutely no documentation - not a single word anywhere except the traceback of GB options in mdout.mdp (that is how I found this out). Is this feature still experimental? Where can I read about the method implemented? Thanks in advance! Semen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
