[gmx-users] Problem in the gromacs git version
Fabrizio Marinelli
marinell at sissa.it
Fri Apr 30 11:25:11 CEST 2010
Just to add more information, i have tried with the gromacs-4.0.5 and the
force field GROMOS96 43a1, and in this case it is everything ok, SR are
not 0. This means that probably there must be something wrong with the
gromacs git version.
Fabrizio
> 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 simulation
> even 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?
> Thanks again,
> Fabrizio
>
>>
>>
>> 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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>>>
>>>
>>>
>>> ----------------------------------------------------------------
>>> 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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