Here is the command: g_order_d_mpi -f 265K_50_50_50_2-pbcfixed.xtc -n wateroxygens.ndx -s 265K_50_50_50_2.tpr -o Sg265K
On Tue, 2010-08-31 at 21:15 +0200, David van der Spoel wrote: > On 2010-08-31 21.10, Paymon Pirzadeh wrote: > > Yes, > > I tried it, but I run into segmentation fault. Here is part of the error > > message: > > > > WARNING: distance between atoms 4869 and 0> 0.3 nm (3.515866). Index > > file might be corrupt. > > WARNING: distance between atoms 4870 and 0> 0.3 nm (3.580329). Index > > file might be corrupt. > > WARNING: distance between atoms 4871 and 0> 0.3 nm (3.489775). Index > > file might be corrupt. > > WARNING: distance between atoms 4872 and 0> 0.3 nm (3.464816). Index > > file might be corrupt. > > WARNING: distance between atoms 4873 and 0> 0.3 nm (3.561426). Index > > file might be corrupt. > > Segmentation fault > > > what command line are you using? > > > > > I thought it might be a periodic boundary issue, so I issued: > > trjconv_d_mpi -f 265K_50_50_50_2.xtc -o 265K_50_50_50_2-pbcfixed -pbc > > whole -s 265K_50_50_50_2.tpr > > > > but the problem still persists. Any tips? > > Regards, > > > > Paymon > > > > > > > > > > > > On Tue, 2010-08-31 at 20:37 +0200, David van der Spoel wrote: > >> On 2010-08-31 20.26, Paymon Pirzadeh wrote: > >>> Hello, > >>> It is said in the mannual that g_order compute the order parameter per > >>> atom for carbon tails. Can it also calculate order (degree of > >>> tetrahedrality) for water molecules if only water oxygens are selected > >>> in index file? The reference paper is for water molecules though. Also, > >>> does it calculate an average value or give a profile as a function of > >>> time? > >>> thanks, > >>> > >>> Paymon > >>> > >> Have you tried it? > >> > >> You can compute tetrahedrality for water, and also do it in slices > >> accross the box axis. It computes the average over time. > >> > >> -- > >> 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.se http://folding.bmc.uu.se > > > > > -- > 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.se 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/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
