Hi Good point. The environment variable names changed.
Thus $GMX_QM_MODIFIED_LINKS_DIR is what used to be DEVIL_DIR The same for the others. Gerrit > Good 4. Re: Gromacs2019 + Gaussian09 QMMM (nikol...@spbau.ru) > > > Dear Gerrit, > > Thank you very much for your answer. > As I understand, I do not to modify links if I use gau script. > I have put the gau script (with all necessary modifications) into folder > ~/test/gau > export GAUSS_DIR=~/test/gau > export GAUSS_EXE=gau > Created the empty directory ~/test/devil > export DEVIL_DIR=~/test/devil > > However, mdrun still fails with the following error: > > Fatal error: > no $GMX_QM_MODIFIED_LINKS_DIR, this is were the modified links reside. > > > What am I doing wrong? > > Best, > Dmitrii > > > > > > >> >> Dear Dmitrii, >> >> Unfortunately, the group nb-search scheme that was needed for QM/MM is >> discontinued. Because it still worked in the 2018 version, I suggest that >> you use the previous version until the problem is fixed. >> >> Use >> -DGMX_QMMM_PROGRAM=gaussian >> in the cmake command to compile with support. Details on how to link >> gaussian09 can be found here: >> http://wwwuser.gwdg.de/~ggroenh/qmmm.html#gaussian >> It probably is easiest to use the gau script to make the two programs talk >> to each other. >> >> Good luck, >> >> Gerrit >> >> >> >> ________________________________ >> >> >> Dear all, >> >> I am planning to run QM/MM dynamics (ONIOM), following the approach >> described here >> http://manual.gromacs.org/2019/reference-manual/special/qmmm.html#output >> >> (not the MiMiC, because it has only an additive scheme), Gaussian09 as the >> QM package. >> >> However, I could not find any information on compilation of gromacs 2019 >> with Gaussian, only CP2K for MiMiC support: >> >> http://manual.gromacs.org/documentation/2019/install-guide/index.html >> >> Where I can find the information on the Gromacs2019+Gaussian09 QMMM >> installation? >> >> Best, >> Dmitrii >> >> >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send >> a mail to gmx-users-requ...@gromacs.org. >> > > > > > ------------------------------ > > Message: 5 > Date: Sat, 5 Oct 2019 23:28:55 +0530 > From: Quin K <profiles...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] RMSD analysis of protein-ligand complex > Message-ID: > <CAG0e8MMjQPR=rwrb5d5besyvbnabqywltbsutfbkmofm-fu...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Thank you. > > I examined the trajectory using VMD and noted that ligand had come out of > the binding site and is running around. > How is this possible? I have used the guidelines in mdtutorials.com to set > up the system. > However it's worth noting that there was a power failure around the same > time (23ns) and I had to restart MD with append command. > Could this have had an affect on MD? Do I have to recreate trajectory file > after restarting MD, instead of using the default trajectory? > > Regards > > On Sat, Oct 5, 2019 at 9:53 PM Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 10/5/19 11:59 AM, Quin K wrote: >>> Thank you. >>> >>> I got following when I analysed Ligand RMSD protein backbone as east >> square >>> fit. >>> Graph <https://photos.app.goo.gl/JZJaLt1BxJi1qgwV7> >>> Can you please comment why there's high fluctuation after like 23 ns? >>> What could this mean? >> >> Watch the trajectory and see what is going on. Make sure you've properly >> re-imaged to account for PBC effects. >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Office: 301 Fralin Hall >> Lab: 303 Engel Hall >> >> Virginia Tech Department of Biochemistry >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalem...@vt.edu | (540) 231-3129 >> http://www.thelemkullab.com >> >> ================================================== >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 186, Issue 12 > ****************************************************** -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.