[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.

[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

[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

[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