[gmx-users] g_sdf gives wrong refmol with multiple center molecules
Hi, if you give g_sdf just one molecule (in mode 1) to look at the distribution of other atoms around it, everything looks fine. However, if you give two or more molecules, the refmol.gro that is printed is messed up, but the actual density map still looks ok. You can try this with the 216 water molecule tutorial case. Run a short md writing frames into traj.xtc. Append these lines to the index.ndx (which has only OW group before these). [ O1 ] 1 4 [ H1 ] 2 5 [ H2 ] 3 6 or [ O1 ] 1 [ H1 ] 2 [ H2 ] 3 give g_sdf -s topol.tpr -f traj.xtc -n index.ndx -r 2 3 4 1 and have a look at the refmol.gro in the two cases. Is there something wrong in adding up the coordinates? Cheers, Atte ___ 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] Running Gromacs on the Grid Workshop 14.-15.11.
Running Gromacs on the Grid 14.-15.11., at CSC, Espoo, Finland. CSC will organise a workshop to show how to run Gromacs jobs in MGrid and other NorduGrid clusters. The hands-on examples are chosen to illustrate how to use simultaneous serial simulations effectively and that methodology is, of course, usable also outside ARC-based grids. Gromacs developers Erik Lindahl and Berk Hess and Grid specialists from CSC are available to answer your questions and tutor the hands-on exercises. The Workshop is sponsored by NDGF (Nordic Data Grid Facility) and participants from Scandinavia and the Baltic region have precedence. The registration ends by Monday 5th November at 12:00 so be quick! Registration and more information: http://www.csc.fi/english/csc/courses/archive/Grid-gmx07 Cheers, Atte -- Atte Sillanpää, Application specialist, Chemistry Support CSC - IT Center of Science, Po Box 405, 02101 Espoo, FINLAND TEL +358 9 457 2250, www.csc.fi, email [EMAIL PROTECTED]___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] short range nonbondeds = 0 in power4
On Fri, 15 Sep 2006, Atte Sillanpää wrote: I've run into a mysterious problem. The versions 3.3. and 3.3.1 compile and execute, but the short range coulomb and LJ energies come out as zero when using the mpi-version. Serial code works ok (mpi version gives zero if run using just one cpu). No errors, no warnings. Hi, the problem seems solved. I removed the --enable-threads from the gromacs config options and now short range forces come out right. Simulations are stable and e.g. water rdfs are identical in power4 and amd opteron. It's a little bit nasty that compiler gets through the threads flag but then computes garbage. It has been said in the mailing list that threads don't work yet, but that's hard to find as the solution unless you know to look for it. To further check my binary I'd like to do some other tests. I tried looking for the benchmarks, but the link doesn't work (search for 'bench' at the gromacs site). Are they still available (and do they have some verified results to compare to?) Thanks, Atte___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] short range nonbondeds = 0 in power4
Hi, I've run into a mysterious problem. The versions 3.3. and 3.3.1 compile and execute, but the short range coulomb and LJ energies come out as zero when using the mpi-version. Serial code works ok (mpi version gives zero if run using just one cpu). No errors, no warnings. I've tried using both fftw 2.1.5 and 3.0.1, tried dropping the optimization level to -O1, -qstrict, --disable-ppc-altivec, ... The config options were (e.g.) as follows: setenv CPPFLAGS -I/v/aix52_rs/appl/math/fftw/fftw-3.0.1_32/include setenv LDFLAGS -L/v/aix52_rs/appl/math/fftw/fftw-3.0.1_32/lib setenv MPICC mpcc_r ./configure --prefix=/wrk/gmx --program-suffix=_mpi --enable-mpi --disable-nice --enable-threads -with-fft=fftw3 From the beginning of the config.log: hostname = p690m uname -m = 00105CDA4C00 uname -r = 2 uname -s = AIX uname -v = 5 /usr/bin/uname -p = powerpc /bin/uname -X = unknown /bin/arch = unknown /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown hostinfo = unknown /bin/machine = unknown /usr/bin/oslevel = 5.2.0.0 /bin/universe = unknown We don't get the kind of errors described earlier for power4 on the list. I actually managed to make a working mdrun_mpi from 3.3 last year using the same options, but after poe/ppe/... update on the power4 machine I get this odd behaviour also on the 3.3 version. Any ideas? What to tweak, where to look? Cheers, Atte ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
