[gmx-users] Problem in the gromacs git version: SOURCE FOUND
Roland Schulz
roland at utk.edu
Fri Apr 30 18:26:55 CEST 2010
Hi,
bugs should be reported to bugzilla.gromacs.org. This way they are not
forgotten.
Roland
On Fri, Apr 30, 2010 at 7:12 AM, Fabrizio Marinelli <marinell at sissa.it>wrote:
> Hi all, i have found the source of the error. I was compiling the latest
> gromacs git version using the option --enable-fortran during the
> configuration, this for the system i used (even the simple 216 spc box)
> and for a generic force field gives SR interactions = 0.
> Eliminating the option --enable-fortran everything works and the energies
> are the same of gromacs-4.0.5.
> This maybe useful for some of you.
> Best,
> Fabrizio
>
> >
> >
> > ----- Original Message -----
> > From: Fabrizio Marinelli <marinell at sissa.it>
> > Date: Friday, April 30, 2010 19:17
> > Subject: [gmx-users] Problem in the gromacs git version
> > To: jalemkul at vt.edu, Discussion list for GROMACS users
> > <gmx-users at gromacs.org>
> >
> >> Hi all,
> >> i have downloaded and installed the latest gromacs git version
> >> with the
> >> purpose of testing the charmm force field. I noticed that with
> >> pdb2gmx i
> >> am able to construct the topology without problems and also to
> >> run the
> >> simulation. Then when i look to the energy terms i notice that SR
> >> interaction are 0 and this of course generate problems to the
> >> simulationeven if it does not crush. I also tried with the
> >> GROMOS96 43a1 force field
> >> and it gives the same. I also tried to remove the protein and
> >> run only
> >> water molecules and still SR are 0. I tried also to run the
> >> simulation of
> >> spc216.gro water box, and it still gives the same.
> >> Does any one of you faced with the same problem? If not, could
> >> some you
> >> try the same test to see if you find the same? Could some of you
> >> eventually propose a solution?
> >
> > I was using git master this week without observing such a problem.
> >
> > Two approaches to a solution occur to me. Either vary your .mdp entries
> > until it works, which can identify the broken algorithm, or, use git to
> go
> > back in time until you find a point where the simulation works. Then the
> > erroneous commit, if any, can be found.
> >
> > What's best will depend why you're using the git version.
> >
> > Mark
> >
> >> > Fabrizio Marinelli wrote:
> >> >> Here it is my .mdp file, i attach you also the topology file,
> >> just to be
> >> >> more specific the one that are 0 are the SR interactions,
> >> thank you very
> >> >> much.
> >> >
> >> > For diagnostic purposes, can you re-process your structure
> >> using a
> >> > different
> >> > force field and try again? If the energies are still
> >> coming up zero, then
> >> > there
> >> > may be something wrong in the code as a whole, otherwise it is
> >> specific to
> >> > the
> >> > CHARMM force field. Either way, I'm out of my league on
> >> this one :)
> >> > Maybe a
> >> > developer can comment.
> >> >
> >> > -Justin
> >> >
> >> >> Fabrizio
> >> >>
> >> >>
> >> title = Teaa MD
> >> >>
> >> cpp = /lib/cpp
> >> >>
> >> include =
> >> >>
> >> integrator = md
> >> >>
> >> comm_mode = Linear
> >> >>
> >> nstcomm = 10
> >> >>
> >> tinit = 0
> >> >> comm-
> >> grps = System
> >> >>
> >> dt = 0.002
> >> >>
> >> nsteps = 6000000
> >> >> ; OUTPUT CONTROL OPTIONS =
> >> >> ; Output frequency for coords (x), velocities (v) and forces
> >> (f) =
> >> >>
> >> nstxout = 5000
> >> >>
> >> nstvout = 5000
> >> >> ; Output frequency for energies to log file and energy file =
> >> >>
> >> nstlog = 500
> >> >>
> >> nstenergy = 500
> >> >>
> >> nstxtcout = 500
> >> >> xtc-
> >> precision = 100000
> >> >>
> >> xtc_grps = System
> >> >>
> >> energygrps = System
> >> >>
> >> pbc = xyz
> >> >>
> >> nstlist = 5
> >> >>
> >> epsilon_r = 1.
> >> >>
> >> ns_type = grid
> >> >>
> >> coulombtype = pme
> >> >>
> >> vdwtype = Cut-Off
> >> >>
> >> fourierspacing = 0.12
> >> >> ; EWALD/PME/PPPM parameters
> >> >>
> >> pme_order = 4
> >> >>
> >> ewald_rtol = 2.2e-05
> >> >>
> >> epsilon_surface = 0
> >> >>
> >> optimize_fft = yes
> >> >>
> >> rlist = 1.2
> >> >>
> >> rcoulomb = 1.2
> >> >>
> >> rvdw = 1.2
> >> >>
> >> tcoupl = Berendsen
> >> >> tc-
> >> grps = System
> >> >>
> >> tau_t = 1.0
> >> >>
> >> ref_t = 298
> >> >>
> >> pcoupl = Berendsen
> >> >>
> >> pcoupltype = isotropic
> >> >>
> >> tau_p = 2.5
> >> >>
> >> compressibility = 4.5e-5
> >> >>
> >> ref_p = 1.0
> >> >> ; Dielectric constant of reaction field =
> >> >>
> >> epsilon_rf = 80.0
> >> >>
> >> gen_vel = yes
> >> >>
> >> gen_temp = 298
> >> >>
> >> gen_seed = 173529
> >> >>
> >> constraints = all-bonds
> >> >> constraint_algorithm = lincs
> >> >>
> >> shake_tol = 0.0001
> >> >> ; Highest order in the expansion of the constraint coupling
> >> matrix =
> >> >> lincs-
> >> order = 4
> >> >> ; Lincs will write a warning to the stderr if in one step a
> >> bond =
> >> >> ; rotates over more degrees than =
> >> >> lincs-
> >> warnangle = 30
> >> >> user1-
> >> grps = System
> >> >> ; Non-equilibrium MD stuff =
> >> >> acc-
> >> grps =
> >> >>
> >> accelerate =
> >> >>
> >> freezegrps =
> >> >>
> >> freezedim =
> >> >> cos-
> >> acceleration =
> >> >>
> >> >>
> >> >>>
> >> >>> Fabrizio Marinelli wrote:
> >> >>>> Hi all,
> >> >>>> I have downloaded the latest git version of gromacs
> >> (yesterday) in
> >> >>>> which
> >> >>>> it is possible to use the charmm27 force field, I
> >> constructed the
> >> >>>> topology
> >> >>>> for my protein using the pdb2gmx program, everything goes
> >> ok also with
> >> >>>> the
> >> >>>> solvation, but then when i run the MD i notice that coulomb
> >> and LJ
> >> >>>> interaction are 0 and also the protein consequently unfold.
> >> >>>> Did any of you found this kind of problem? Could some of
> >> you rpopose
> >> >>>> eventually a solution?
> >> >>> Can you post your .mdp file?
> >> >>>
> >> >>> -Justin
> >> >>>
> >> >>>> Thanks in advance,
> >> >>>> Fabrizio
> >> >>>>
> >> >>>>
> >> >>>> ------------------------------------------------------------
> >> ----
> >> >>>> SISSA Webmail https://webmail.sissa.it/
> >> >>>> Powered by SquirrelMail http://www.squirrelmail.org/
> >> >>>>
> >> >>> --
> >> >>> ========================================
> >> >>>
> >> >>> 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 at gromacs.org
> >> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> >>> Please search the archive at http://www.gromacs.org/search before
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> >> >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >> >>>
> >> >>
> >> >>
> >> >>
> >> >> --------------------------------------------------------------
> >> --
> >> >> SISSA Webmail https://webmail.sissa.it/
> >> >> Powered by SquirrelMail http://www.squirrelmail.org/
> >> >
> >> > --
> >> > ========================================
> >> >
> >> > 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
> >> >
> >> > ========================================
> >> > --
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> >> >
> >>
> >>
> >>
> >> ----------------------------------------------------------------
> >> SISSA Webmail https://webmail.sissa.it/
> >> Powered by SquirrelMail http://www.squirrelmail.org/
> >>
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