[gmx-users] Can I generate Pulf files after mD running?
Dear gmx-users, I have just finished umbrella MD but I missed to type pullf/pullx options on mdrun. So, can I get pullf/pullx .xvg files from mdrun results? Best regards, Yoochan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Weird error message from QM/MM run.
QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 30 QMlevel: RHF/STO-3G number of CPUs for gaussian = 1 memory for gaussian = 5000 accuracy in l510 = 8 NOT using cp-mcscf in l1003 Level of SA at start = 0 [yoochancal2-desktop:09740] *** Process received signal *** [yoochancal2-desktop:09740] Signal: Segmentation fault (11) [yoochancal2-desktop:09740] Signal code: Address not mapped (1) [yoochancal2-desktop:09740] Failing at address: (nil) [yoochancal2-desktop:09740] [ 0] /lib/libpthread.so.0 [0x7f3d70cd5080] [yoochancal2-desktop:09740] [ 1] /lib/libc.so.6(strlen+0x30) [0x7f3d709d4c60] [yoochancal2-desktop:09740] [ 2] /lib/libc.so.6(fputs+0x1e) [0x7f3d709bcb3e] [yoochancal2-desktop:09740] [ 3] mdrun(init_gaussian+0x4eb) [0x52709b] [yoochancal2-desktop:09740] [ 4] mdrun(init_QMMMrec+0x10e0) [0x51fb10] [yoochancal2-desktop:09740] [ 5] mdrun(mdrunner+0xf59) [0x435339] [yoochancal2-desktop:09740] [ 6] mdrun(main+0x3da) [0x43bd2a] [yoochancal2-desktop:09740] [ 7] /lib/libc.so.6(__libc_start_main+0xe6) [0x7f3d709725a6] [yoochancal2-desktop:09740] [ 8] mdrun [0x41c4d9] [yoochancal2-desktop:09740] *** End of error message *** Segmentation fault QM/MM (Gaussian 03, Gromacs 4.0.5) I edited gaussian03 link files by under link. http://wwwuser.gwdg.de/~ggroenh/qmmm.html I have no Idea what the error message mean. Any suggestions? regard. yoochan.-- gmx-users mailing listgmx-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
[gmx-users] [ dummies 2] or [ virtual_sites 2] not works.
Hi. I'm on QM/MM simulation (gromacs-gaussian03). I exactly followed under reference, but I could't success. http://wwwuser.gwdg.de/~ggroenh/EMBO2004/html/qmmmvacuum.html#top I checked presence of two LA atoms in [ atoms] of TOP file. Also, I checked under [ dummies 2] and [ constraints ]in Top file. (I think, [ dummies 2] = [ virtual_sites 2] but, [ virtual_sites 2] in 4.x.x Gromacs, [ dummies 2] in 3.x.x) [ dummies 2] 1279 906 904 1 0.72 1280 938 936 1 0.72 [ constraints ] 906 904 2 0.153 938 936 2 0.153 And then, I did GROMPP, I got this error message. (In reference, there is a "run.scr " step which is multiple GROMPP and MDRUN running scripts.) 'Atom type "LA" not found' I think grompp doesn't recognize atom "LA" on [ atoms ] as dummies. Any suggestions? Regards. yoochan,-- gmx-users mailing listgmx-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
[gmx-users] Configuration of Gaussian for QM/MM
Hello. I'm trying to setup QM/MM for Gaussian03. http://wwwuser.gwdg.de/~ggroenh/qmmm.html I refer the upper links, but I still can not understand. ==roadmap.pdf (page 6) modified subroutines in l701 • oneeli added an extra argument to Oneeli() for the forces on the point charges subroutine Oneeli(...,FCh) added to the declaration section Real*8 FCh(*) added an extra argument to all PrsmSu() function calls PrsmSu(...,FCh) ==roadmap.pdf (page 6) gau-fsplit -e d1e l701.F ; works fine gau-fsplit -e oneeli l701.F ; no works. So, I do job on l701.F and I can't find 'subroutine Oneeli ()' either Prsmsu ()' in l701.F. Is there any misunderstand about instruction ? regard. yoochan. -- gmx-users mailing listgmx-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
[gmx-users] "Covariance Matrix" to square matrix.
Hi. I have two questions. 1. How to get Matrix form(readable) of eigenvector (in normal mode analysis) from eigenvector.trr ? 2. I got covariance matrix file "Covar.dat" and there are 3675 x 3 matrix , not 105 x 105 matrix. So, How can I change 3675 x 3 matrix to 105 x 105 ? Regards. yoochan.-- gmx-users mailing listgmx-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
