[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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> 
> 
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