Dear gerrit sir, thank you for your reply Here I have got compilation error as follows
/root/gromacs-4.5.3/src/mdlib/.libs/libmd_d.a(qm_mopac.o): In function `call_mopac_SH': qm_mopac.c:(.text+0x2a7): undefined reference to `domop_' /root/gromacs-4.5.3/src/mdlib/.libs/libmd_d.a(qm_mopac.o): In function `call_mopac': qm_mopac.c:(.text+0x70b): undefined reference to `domop_' /root/gromacs-4.5.3/src/mdlib/.libs/libmd_d.a(qm_mopac.o): In function `init_mopac': qm_mopac.c:(.text+0x964): undefined reference to `domldt_' collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/root/gromacs-4.5.3/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/root/gromacs-4.5.3/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/root/gromacs-4.5.3/src' make: *** [all-recursive] Error 1 i am using the following command ./configure --disable-float --with-qmmm-mopac CPPFLAGS=-DUSE_MOPAC LIBS=-lmopac LDFLAGS=-L/usr/local/lib i am expecting your useful reply Thanks in Advance --- On Tue, 7/12/10, Gerrit Groenhof <ggro...@gwdg.de> wrote: From: Gerrit Groenhof <ggro...@gwdg.de> Subject: [gmx-users] Re: gmx-users Digest, Vol 80, Issue 41 To: gmx-users@gromacs.org Date: Tuesday, 7 December, 2010, 1:24 AM Without-qmmm-mopac will not lead to compilation of the mopac interface source code. What is the compilation error? Gerrit > > 1. MOPAC gromacs mdreun error (vidhya sankar) (vidhya sankar) > > > Message: 1 > Date: Mon, 6 Dec 2010 18:34:00 +0530 (IST) > From: vidhya sankar <scvsankar_...@yahoo.com> > Subject: [gmx-users] MOPAC gromacs mdreun error (vidhya sankar) > To: gmx-users@gromacs.org > Message-ID: <665887.73042...@web95501.mail.in.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Gerrit sir, > Thank you for your atonce reply > my mopac stand alone binary works well i have tested using ./run_mopac7 > tests/force > but mdrun is not properly linked aganist libmopac.a > i am using the following command to configure > ./configure --disable-float --without-qmmm-mopac CPPFLAGS=-DUSE_MOPAC > LIBS=-lmopac LDFLAGS=-L/usr/local/lib > if i use --with-qmmm-mopac i end in make error (compilation error) > also how to check how to check the link of mdrun aganist libmopac.a is >there is any command for this? > i am expecting your precious reply thanks in advance > > > > > > > > > > > > > > > > --- On Mon, 6/12/10, Gerrit Groenhof <ggro...@gwdg.de> wrote: > > From: Gerrit Groenhof <ggro...@gwdg.de> > Subject: Subject: [gmx-users] : MOPAC gromacs mdreun error (vidhya sankar) > To: gmx-users@gromacs.org > Date: Monday, 6 December, 2010, 12:57 PM > > Please check if your stand-alone mopac binary works properly. Also check if > the mdrun binary is linked against the libmopac.a > > Gerrit >> Message: 2 >> Date: Mon, 6 Dec 2010 11:55:58 +0530 (IST) >> From: vidhya sankar<scvsankar_...@yahoo.com> >> Subject: [gmx-users] : MOPAC gromacs mdreun error (vidhya sankar) >> To: gmx-users@gromacs.org >> Message-ID:<157886.66733...@web95506.mail.in.yahoo.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Dear Gerrit sir, >> Thank you for your previous reply i tried as u said with >>-nt 1 option in mdrun but still i have got hte following error when i run >>mdrun_d >> QM/MM calculation requested. >> there we go! >> Layer 0 >> nr of QM atoms 2 >> QMlevel: PM3/STO-3G >> Program mdrun_d, VERSION 4.5.3 >> Source code file: qmmm.c, line: 697 >> Fatal error: >> Semi-empirical QM only supported with Mopac. >> but i configured gromacs properly with mopac. how to solve the problem >> is ther is any link that i have not made available ? i am expecting your >>worthfull reply thanks isn advance >> >> > > -- 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/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 > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20101206/a0dfd1a9/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Mon, 06 Dec 2010 18:40:36 +0100 > From: Sebastian Fritsch <frit...@mpip-mainz.mpg.de> > Subject: Re: [gmx-users] Constraining two virtual sites > To: gmx-users@gromacs.org > Message-ID: <4cfd2014.1080...@mpip-mainz.mpg.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi again, > > > unfortunately I would need the constraint for a large number of molecules, > say ~1000 i.e. 2000 vsites representing a few atoms each. > The constraint length should however be the same for each molecule. > > Assigning groups for each constraint group would not be possible due to the > group limit I guess. > The do_constraint function in pull.c does not look too complicated, do you > think it would be reasonable to adapt it a bit and call it > from some function like calc_bonds which comes after vsite construct and > before vsite spread? The constraint forces in my case should be > be completely determined by the vsites, or am I wrong? Is there an easier > solution? > > > Thank you, > Sebastian > >> Hi, >> >> Unfortunately constraints can not be applied to virtual sites and grompp >> apparently >> does not not check for this. I will add a check. >> Constraints between virtual sites can lead to very complex constraint >> equations >> between the masses involved. Thus the general case if difficult to implement. >> Your cases seems quite simple and could be done with the pull code, >> if it would support more than one reference group, which I was thinking to >> implement. >> >> How many molecules do you have? >> >> Berk >> > > > > ------------------------------ > > Message: 3 > Date: Mon, 06 Dec 2010 13:56:04 -0500 > From: nishap.pa...@utoronto.ca > Subject: [gmx-users] Energy-groups? > To: gmx-users@gromacs.org > Message-ID: <20101206135604.dgzv1f90bk08o...@webmail.utoronto.ca> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Hello, > > I want to plot the interaction potential energy between my solute > and solvent. In my .mdp file I did not mention anything under > energygrps,so I am thinking it calculates the energies for the whole > system. But is there a way I can extract say for example LJ-14 term > between my solute and solvent using the same .edr file? Or would I > have to specify my energygrps and run the simulation again. > > Thanks. > > Nisha > > > > ------------------------------ > > Message: 4 > Date: Mon, 06 Dec 2010 13:59:23 -0500 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] Energy-groups? > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4cfd328b.6040...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > nishap.pa...@utoronto.ca wrote: >> Hello, >> >> I want to plot the interaction potential energy between my solute and >> solvent. In my .mdp file I did not mention anything under energygrps,so >> I am thinking it calculates the energies for the whole system. But is >> there a way I can extract say for example LJ-14 term between my solute >> and solvent using the same .edr file? Or would I have to specify my >> energygrps and run the simulation again. >> > > 1-4 interactions are intramolecular, so there should be no solute-solvent 1-4 > term. If you want nonbonded potentials decomposed, yes, you have to rerun > your > trajectory (mdrun -rerun, not from scratch) with a .tpr file specifying the > desired groups. > > -Justin > >> Thanks. >> >> Nisha >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 5 > Date: Mon, 06 Dec 2010 14:31:38 -0500 > From: nishap.pa...@utoronto.ca > Subject: Re: [gmx-users] Energy-groups? > To: gmx-users@gromacs.org > Message-ID: <20101206143138.irw4yddc6c4gk...@webmail.utoronto.ca> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Quoting "Justin A. Lemkul" <jalem...@vt.edu>: > > Thanks Justin! I do want the non-bonded potential between my solute > and solvent. So in my .mdp file I put my solute and solvent as > energygrps and ran mdrun using this command: > mdrun -s md1.tpr(including energygrps) -rerun md.xtc (my trajectory) > > Is that correct? I don't understand how it would be faster or any > different from running the simulation from scratch, because in my .mdp > file it still has time of 100ns. I just modified the energygrps. > > >> >> >> nishap.pa...@utoronto.ca wrote: >>> Hello, >>> >>> I want to plot the interaction potential energy between my solute >>> and solvent. In my .mdp file I did not mention anything under >>> energygrps,so I am thinking it calculates the energies for the >>> whole system. But is there a way I can extract say for example >>> LJ-14 term between my solute and solvent using the same .edr file? >>> Or would I have to specify my energygrps and run the simulation >>> again. >>> >> >> 1-4 interactions are intramolecular, so there should be no >> solute-solvent 1-4 term. If you want nonbonded potentials decomposed, >> yes, you have to rerun your trajectory (mdrun -rerun, not from scratch) >> with a .tpr file specifying the desired groups. >> >> -Justin >> >>> Thanks. >>> >>> Nisha >>> >> >> -- >> ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- >> 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/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 > > > > > > ------------------------------ > > Message: 6 > Date: Mon, 06 Dec 2010 14:52:05 -0500 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] Energy-groups? > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4cfd3ee5.6020...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > nishap.pa...@utoronto.ca wrote: >> Quoting "Justin A. Lemkul" <jalem...@vt.edu>: >> >> Thanks Justin! I do want the non-bonded potential between my solute and >> solvent. So in my .mdp file I put my solute and solvent as energygrps >> and ran mdrun using this command: >> mdrun -s md1.tpr(including energygrps) -rerun md.xtc (my trajectory) >> >> Is that correct? I don't understand how it would be faster or any >> different from running the simulation from scratch, because in my .mdp >> file it still has time of 100ns. I just modified the energygrps. >> > > It should be significantly faster. In this case, mdrun is not doing the > integration, it's simply using the known positions to re-calculate energies. > > -Justin > >> >>> >>> >>> nishap.pa...@utoronto.ca wrote: >>>> Hello, >>>> >>>> I want to plot the interaction potential energy between my solute >>>> and solvent. In my .mdp file I did not mention anything under >>>> energygrps,so I am thinking it calculates the energies for the whole >>>> system. But is there a way I can extract say for example LJ-14 term >>>> between my solute and solvent using the same .edr file? Or would I >>>> have to specify my energygrps and run the simulation again. >>>> >>> >>> 1-4 interactions are intramolecular, so there should be no >>> solute-solvent 1-4 term. If you want nonbonded potentials decomposed, >>> yes, you have to rerun your trajectory (mdrun -rerun, not from scratch) >>> with a .tpr file specifying the desired groups. >>> >>> -Justin >>> >>>> Thanks. >>>> >>>> Nisha >>>> >>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> -- >>> 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/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 >> >> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > -- > 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/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 80, Issue 41 > ***************************************** -- Gerrit Groenhof MPI biophysical chemistry Goettingen Germany http://wwwuser.gwdg.de/~ggroenh/ -- 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/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 mailing list gmx-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
