[gmx-users] g_rdf -xy
Dear gmx-users, I simulate a vapor/water/decane/vapor interface system. The interface is xy plane. I want to analysis water structure at the interface using g_rdf program along z axis with -xy parameter. But the calculation is hanged as the following: Select a reference group and 1 group Group 0 ( OW) has 2508 elements Group 1 ( HW*) has 5016 elements Select a group: 0 Selected 0: 'OW' Select a group: 0 Selected 0: 'OW' trn version: GMX_trn_file (single precision) Skipping frame 3000 time 4100.000 I used the following the operation g_rdf -f -s -n -bin 100 -xy -o Is the runing normal? Please give me some suggestion. Thanks a lot! H.Y. Xiao ___ 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] g_rdf -xy
Hi, g_rdf -xy does not do what you want. It determines rdf's using only the x and y components of the distance and averages over z. g_rdf hangs probably because you use -nbin 100, which sets bins with a width of 100 nm (and not 100 bins as you probably thought). There is currently no Gromacs tools which can easily do what you want. Berk Date: Mon, 18 May 2009 16:12:16 +0800 From: hyx...@mail.ipc.ac.cn To: gmx-users@gromacs.org Subject: [gmx-users] g_rdf -xy Dear gmx-users, I simulate a vapor/water/decane/vapor interface system. The interface is xy plane. I want to analysis water structure at the interface using g_rdf program along z axis with -xy parameter. But the calculation is hanged as the following: Select a reference group and 1 group Group 0 ( OW) has 2508 elements Group 1 ( HW*) has 5016 elements Select a group: 0 Selected 0: 'OW' Select a group: 0 Selected 0: 'OW' trn version: GMX_trn_file (single precision) Skipping frame 3000 time 4100.000 I used the following the operation g_rdf -f -s -n -bin 100 -xy -o Is the runing normal? Please give me some suggestion. Thanks a lot! H.Y. Xiao _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ 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] g_rdf -xy
Dear Berk, I am sorry that I have a mistake in the first letter. In fact I used -bin 0.05, not 100. Yet the result is hanged. Maybe as you said, the current Gromacs can not realize what I want to do. Thanks again! H.Y. Xiao ___ 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
