I tried the -Sg and it worked. Thanks. But, I used -Sgsl for a spatial profile and it looks like that it is not a valid option. I tried the following: g_order_d_mpi -f Ih0001_54_62_102.xtc -n wateroxygens.ndx -s Ih0001_54_62_102.tpr -os Ih0001_54_62_102-sg -sl 100 -d z
but I ran into the previous segmentation fault. If I just use the Sg, just the temporal profile is generated which is not what I want. Sorry for mass of e-mails, but any tips on that? Paymon On Tue, 2010-08-31 at 21:49 +0200, David van der Spoel wrote: > On 2010-08-31 21.19, Paymon Pirzadeh wrote: > > 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 > You need to replace -o by one of > -Sg sg-ang.xvg Output, Opt. xvgr/xmgr file > -Sk sk-dist.xvg Output, Opt. xvgr/xmgr file > -Sgsl sg-ang-slice.xvg Output, Opt. xvgr/xmgr file > -Sksl sk-dist-slice.xvg Output, Opt. xvgr/xmgr file > > > > > > > > > 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 > > > > > -- > 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
