[gmx-users] Re: eg compilation problem in Mopac gromacs (vidhya sankar)
Gerrit Groenhof
ggroenh at gwdg.de
Wed Sep 8 09:13:08 CEST 2010
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_agr at yahoo.com>
> Subject: [gmx-users] reg compilation problem in Mopac gromacs
> To: gmx-users at gromacs.org
> Message-ID: <680789.9939.qm at 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
>
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> ------------------------------
>
> Message: 2
> Date: Wed, 08 Sep 2010 15:27:25 +1000
> From: Dallas Warren <Dallas.Warren at monash.edu>
> Subject: RE: [gmx-users] Alanine dipeptide simulations
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <39D19992D8A3804B8C801976ACB4596255F9D9 at 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.warren at 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-bounces at gromacs.org
> [mailto:gmx-users-bounces at 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.warren at 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-bounces at gromacs.org
> [mailto:gmx-users-bounces at 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.
>
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> ------------------------------
>
> Message: 3
> Date: Wed, 8 Sep 2010 01:38:02 -0400
> From: Sai Pooja <saipooja at gmail.com>
> Subject: Re: [gmx-users] Alanine dipeptide simulations
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <AANLkTi=BPb+L3COHkOdgW004ED35PagtwPqPAq4dwoFu at 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.Warren at 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.warren at 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-bounces at gromacs.org [mailto:
>> gmx-users-bounces at 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.warren at 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-bounces at gromacs.org [mailto:
>> gmx-users-bounces at 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 at 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
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>>
>
>
>
> --
> Quaerendo Invenietis-Seek and you shall discover.
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> End of gmx-users Digest, Vol 77, Issue 45
> *****************************************
--
Gerrit Groenhof
MPI biophysical chemistry
Goettingen
Germany
http://wwwuser.gwdg.de/~ggroenh/
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