[gmx-users] Problem in the gromacs git version
Mark Abraham
mark.abraham at anu.edu.au
Fri Apr 30 11:33:14 CEST 2010
----- 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
> >>>
> >>> ========================================
> >>> --
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> >>>
> >>
> >>
> >>
> >> --------------------------------------------------------------
> --
> >> 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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