You need to compile the mopac library with the modified interface routines and link this library. Use the LDFLAGS and LIBS.
Gerrit > > Today's Topics: > > 1. reg compilation problem in Mopac gromacs (vidhya sankar) > 2. RE: Alanine dipeptide simulations (Dallas Warren) > 3. Re: Alanine dipeptide simulations (Sai Pooja) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 8 Sep 2010 10:50:49 +0530 (IST) > From: vidhya sankar <scvsankar_...@yahoo.com> > Subject: [gmx-users] reg compilation problem in Mopac gromacs > To: gmx-users@gromacs.org > Message-ID: <680789.9939...@web95503.mail.in.yahoo.com> > Content-Type: text/plain; charset="utf-8" > > Dear sir, > thanks in advance > When i type the following command in gromacs directory > ./configure --with-qmmm-mopac --disable-float > it configure successfully > but when i compile by make command i got the following error at the end of my > compilation > > libs/libgmxpreprocess_d.a ../mdlib/.libs/libmd_d.a > /root/gromacs-4.0.5/src/gmxlib/.libs/libgmx_d.a ../gmxlib/.libs/libgmx_d.a > -lnsl -lfftw3 -lm -lmopac -ltest > ../mdlib/.libs/libmd_d.a(qm_mopac.o): In function `call_mopac_SH': > qm_mopac.c:(.text+0x2a7): undefined reference to `domop_' > ../mdlib/.libs/libmd_d.a(qm_mopac.o): In function `call_mopac': > qm_mopac.c:(.text+0x70b): undefined reference to `domop_' > ../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-4.0.5/src/kernel' > make[2]: *** [all-recursive] Error 1 > make[2]: Leaving directory `/root/gromacs-4.0.5/src' > make[1]: *** [all] Error 2 > make[1]: Leaving directory `/root/gromacs-4.0.5/src' > make: *** [all-recursive] Error 1 > What should i do to avoid this error? i am expecting your reply > also when i use ./configure --without-qmmm-mopac --disable-float it compiles > successfully > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100908/a45d777d/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Wed, 08 Sep 2010 15:27:25 +1000 > From: Dallas Warren <dallas.war...@monash.edu> > Subject: RE: [gmx-users] Alanine dipeptide simulations > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <39d19992d8a3804b8c801976acb4596255f...@prk-exch-01.vcp.local> > Content-Type: text/plain; charset="us-ascii" > > See http://www.gromacs.org/Documentation/Terminology/Pressure for > further details > > > > Catch ya, > > Dr. Dallas Warren > > Medicinal Chemistry and Drug Action > > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3010 > dallas.war...@monash.edu > > +61 3 9909 9304 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble > a nail. > > > > From: gmx-users-boun...@gromacs.org > [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Dallas Warren > Sent: Wednesday, 8 September 2010 3:21 PM > To: Discussion list for GROMACS users > Subject: RE: [gmx-users] Alanine dipeptide simulations > > > > What pressure has it reached? > > > > Probably best graph the pressure versus time plot for the run and show > that. > > > I suspect what you are concerned about is the fact that with pressure > coupling, the pressure can fluctuation from step to step, very widely, > 100s atm is not out of the question. > > > > Catch ya, > > Dr. Dallas Warren > > Medicinal Chemistry and Drug Action > > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3010 > dallas.war...@monash.edu > > +61 3 9909 9304 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble > a nail. > > > > From: gmx-users-boun...@gromacs.org > [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Sai Pooja > Sent: Wednesday, 8 September 2010 3:18 PM > To: Discussion list for GROMACS users > Subject: [gmx-users] Alanine dipeptide simulations > > > > Hi, > > I am running an npt simulation on alanine dipeptide in explicit solvent > using charmm forcefield and tip3p. > > The pressure is set to 1bar and the barostat is Parrinello-Rahman. The > simulation has been running for 45 ns and has not achieved the target > average pressure of 1 bar. > > I don;t understand why is this the case. > > My mdp file: > > ; RUN CONTROL PARAMETERS > integrator = md > dt = 0.002 > nsteps = 500000 > > ; OUTPUT CONTROL OPTIONS > nstxout = 0 ; No output, except for > last frame (coordinates) > nstvout = 0 ; No output, except for > last frame (velocities) > nstfout = 0 ; No output, except for > last frame (forces) > nstlog = 5000 ; Write every step to the > log > nstenergy = 5000 ; Write energies at > every step > xtc_grps = Protein SOL > nstxtcout = 5000 ; Do not write a > compressed trajectory > energygrps = Protein SOL ; Write energy information > separately for these groups > > ; NEIGHBORSEARCHING PARAMETERS > nstlist = 5 > ns-type = Grid > pbc = xyz > rlist = 0.9 > > ; OPTIONS FOR ELECTROSTATICS AND VDW > coulombtype = PME > fourierspacing = 0.15 > rcoulomb = 0.9 > vdw-type = Cut-off > rvdw = 1.0 > > ; FFT grid size, when a value is 0 fourierspacing will be used = > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > ; EWALD/PME/PPPM parameters = > pme_order = 4 > ewald_rtol = 1e-05 > epsilon_surface = 0 > optimize_fft = no > ; Temperature coupling > tcoupl = nose-hoover > tc-grps = Protein Non-Protein > tau_t = 0.2 0.2 > ref_t = 300 300 > > ; Pressure coupling > Pcoupl = Parrinello-Rahman > Pcoupltype = Isotropic > tau_p = 1.0 > compressibility = 4.5e-5 > ref_p = 1.0 > > ; OPTIONS FOR BONDS > constraints = all-bonds > > > Pooja > > > > > -- > Quaerendo Invenietis-Seek and you shall discover. > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100908/e2fb02db/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Wed, 8 Sep 2010 01:38:02 -0400 > From: Sai Pooja <saipo...@gmail.com> > Subject: Re: [gmx-users] Alanine dipeptide simulations > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <aanlkti=bpb+l3cohkodgw004ed35pagtwpqpaq4dw...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi > > Yes, the fluctuations are large but even the average pressure hasn't > converged. Its close 2.5 bar. RMSD ~600 bar. > > Pooja > > On Wed, Sep 8, 2010 at 1:27 AM, Dallas Warren <dallas.war...@monash.edu>wrote: > >> See http://www.gromacs.org/Documentation/Terminology/Pressure for further >> details >> >> >> >> Catch ya, >> >> Dr. Dallas Warren >> >> Medicinal Chemistry and Drug Action >> >> Monash Institute of Pharmaceutical Sciences, Monash University >> 381 Royal Parade, Parkville VIC 3010 >> dallas.war...@monash.edu >> >> +61 3 9909 9304 >> --------------------------------- >> When the only tool you own is a hammer, every problem begins to resemble a >> nail. >> >> >> >> *From:* gmx-users-boun...@gromacs.org [mailto: >> gmx-users-boun...@gromacs.org] *On Behalf Of *Dallas Warren >> *Sent:* Wednesday, 8 September 2010 3:21 PM >> >> *To:* Discussion list for GROMACS users >> *Subject:* RE: [gmx-users] Alanine dipeptide simulations >> >> >> >> What pressure has it reached? >> >> >> >> Probably best graph the pressure versus time plot for the run and show >> that. >> >> >> I suspect what you are concerned about is the fact that with pressure >> coupling, the pressure can fluctuation from step to step, very widely, 100s >> atm is not out of the question. >> >> >> >> Catch ya, >> >> Dr. Dallas Warren >> >> Medicinal Chemistry and Drug Action >> >> Monash Institute of Pharmaceutical Sciences, Monash University >> 381 Royal Parade, Parkville VIC 3010 >> dallas.war...@monash.edu >> >> +61 3 9909 9304 >> --------------------------------- >> When the only tool you own is a hammer, every problem begins to resemble a >> nail. >> >> >> >> *From:* gmx-users-boun...@gromacs.org [mailto: >> gmx-users-boun...@gromacs.org] *On Behalf Of *Sai Pooja >> *Sent:* Wednesday, 8 September 2010 3:18 PM >> *To:* Discussion list for GROMACS users >> *Subject:* [gmx-users] Alanine dipeptide simulations >> >> >> >> Hi, >> >> >> I am running an npt simulation on alanine dipeptide in explicit solvent >> using charmm forcefield and tip3p. >> >> The pressure is set to 1bar and the barostat is Parrinello-Rahman. The >> simulation has been running for 45 ns and has not achieved the target >> average pressure of 1 bar. >> >> I don;t understand why is this the case. >> >> My mdp file: >> >> ; RUN CONTROL PARAMETERS >> integrator = md >> dt = 0.002 >> nsteps = 500000 >> >> ; OUTPUT CONTROL OPTIONS >> nstxout = 0 ; No output, except for >> last frame (coordinates) >> nstvout = 0 ; No output, except for >> last frame (velocities) >> nstfout = 0 ; No output, except for >> last frame (forces) >> nstlog = 5000 ; Write every step to the >> log >> nstenergy = 5000 ; Write energies at >> every step >> xtc_grps = Protein SOL >> nstxtcout = 5000 ; Do not write a >> compressed trajectory >> energygrps = Protein SOL ; Write energy information >> separately for these groups >> >> ; NEIGHBORSEARCHING PARAMETERS >> nstlist = 5 >> ns-type = Grid >> pbc = xyz >> rlist = 0.9 >> >> ; OPTIONS FOR ELECTROSTATICS AND VDW >> coulombtype = PME >> fourierspacing = 0.15 >> rcoulomb = 0.9 >> vdw-type = Cut-off >> rvdw = 1.0 >> >> ; FFT grid size, when a value is 0 fourierspacing will be used = >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> ; EWALD/PME/PPPM parameters = >> pme_order = 4 >> ewald_rtol = 1e-05 >> epsilon_surface = 0 >> optimize_fft = no >> ; Temperature coupling >> tcoupl = nose-hoover >> tc-grps = Protein Non-Protein >> tau_t = 0.2 0.2 >> ref_t = 300 300 >> >> ; Pressure coupling >> Pcoupl = Parrinello-Rahman >> Pcoupltype = Isotropic >> tau_p = 1.0 >> compressibility = 4.5e-5 >> ref_p = 1.0 >> >> ; OPTIONS FOR BONDS >> constraints = all-bonds >> >> >> Pooja >> >> >> >> >> -- >> Quaerendo Invenietis-Seek and you shall discover. >> >> -- >> 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 >> > > > > -- > Quaerendo Invenietis-Seek and you shall discover. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100908/33d9d644/attachment.html > > ------------------------------ > > -- > 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 77, Issue 45 > ***************************************** -- 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