[gmx-users] Problem in the gromacs git version
Fabrizio Marinelli
marinell at sissa.it
Fri Apr 30 11:40:58 CEST 2010
Hi Mark, can you send me your .mdp file to compare with mine?
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/
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>> >>>>
>> >>> --
>> >>> ========================================
>> >>>
>> >>> 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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>> >> 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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