[gmx-users] Inconsistent results in different clusters and cores
tarak karmakar
tarak20489 at gmail.com
Fri May 17 12:20:25 CEST 2013
I have read the 'implementation of charmm in gromacs' by bjelkmar,
JCTC. There they have used following cut-offs
coulombtype=PME
rcoulomb=1.2
vdwtype=switch
rvdw=1.2
rvdw-switch=1.0
I am not sure about rlist.
Regards,
Tarak
On Fri, May 17, 2013 at 1:46 PM, tarak karmakar <tarak20489 at gmail.com> wrote:
> Now if I increase the rlist it is showing that
>
> With coulombtype = PME, rcoulomb must be equal to rlist
> If you want optimal energy conservation or exact integration
> use PME-Switch
>
> I don't know exactly what will be the best set up with charmm force field.
>
> Any suggestion please!!
>
> Thanks,
>
> Tarak
>
>
>
>
> On Fri, May 17, 2013 at 1:34 PM, tarak karmakar <tarak20489 at gmail.com>
> wrote:
>>
>> What about Dispersion Correction ?
>> But if I use this set of informations
>>
>> ; 7.3.3 Run Control
>> integrator = md ; md integrator
>> tinit = 0 ; [ps] starting time for
>> run
>> dt = 0.001 ; [ps] time step for
>> integration
>> nsteps = 5000000 ; maximum number of steps
>> to integrate, 0.001 * 50,00,000 =5 ns
>> nstcomm = 1 ; [steps] frequency of
>> mass motion removal
>> comm_grps = system ; group(s) for center of
>> mass motion removal
>>
>> comm_mode = linear
>>
>>
>> ; 7.3.8 Output Control
>> nstxout = 5000 ; [steps] freq to write coordinates
>> to trajectory
>> nstvout = 5000 ; [steps] freq to write velocities to
>> trajectory
>> nstfout = 5000 ; [steps] freq to write forces to
>> trajectory
>> nstlog = 1000 ; [steps] freq to write energies
>> to log file
>> nstenergy = 1000 ; [steps] freq to write energies
>> to energy file
>> nstxtcout = 1000 ; [steps] freq to write
>> coordinates to xtc trajectory
>> xtc_precision = 1000 ; [real] precision to write xtc
>> trajectory
>> xtc_grps = System ; group(s) to write to xtc
>> trajectory
>> energygrps = protein ligand
>>
>> ; 7.3.9 Neighbor Searching
>> nstlist = 10 ; [steps] freq to update neighbor
>> list
>> ns_type = grid ; method of updating neighbor list
>> pbc = xyz ; periodic boundary conditions in
>> all directions
>> rlist = 1.2 ; [nm] cut-off distance for the
>> short-range neighbor list
>> rlistlong = 1.4
>>
>> ; 7.3.10 Electrostatics
>> coulombtype = PME ; Particle-Mesh Ewald
>> electrostatics
>> rcoulomb = 1.2 ; [nm] distance for Coulomb
>> cut-off
>> fourierspacing = 0.16 ; [nm] grid spacing for FFT grid
>> when using PME
>> pme_order = 4 ; interpolation order for PME, 4 =
>> cubic
>> ewald_rtol = 1e-5 ; relative strength of
>> Ewald-shifted potential at rcoulomb
>>
>> ; 7.3.11 VdW
>> vdwtype = switch ; twin-range cut-off with rlist
>> where rvdw >= rlist
>> rvdw = 1.2 ; [nm] distance for LJ cut-off
>> rvdw-switch = 1.0
>>
>> DispCorr = Ener ; apply long range dispersion
>> corrections for energy
>>
>>
>> ; 7.3.14 Temperature Coupling
>> tcoupl = nose-hoover ; temperature coupling
>> tc_grps = system ; groups to couple seperately to
>> temperature bath
>> tau_t = 1.0 ; [ps] time constant for coupling
>> ref_t = 300 ; [K] reference temperature for
>> coupling
>>
>> ; 7.3.15 Pressure Coupling
>> pcoupl = parrinello-rahman ; pressure coupling where
>> box vectors are variable
>> pcoupltype = isotropic ; pressure coupling in
>> x-y-z directions
>> tau_p = 1.0 ; [ps] time constant for
>> coupling
>> compressibility = 4.5e-5 ; [bar^-1] compressibility
>> ref_p = 1.0 ; [bar] reference pressure
>> for coupling
>>
>> gen_vel = yes ; velocity generation
>>
>> gen_temp = 300
>> gen_seed = 8877691
>>
>> ; 7.3.18 Bonds
>> constraints = h-bonds ; covalent h-bonds constraints
>> constraint_algorithm = LINCS ; LINear Constraint Solver
>> continuation = yes ; apply constraints to the start
>> configuration
>> lincs_order = 4 ; highest order in the expansion
>> of the contraint coupling matrix
>> lincs_iter = 1 ; number of iterations to correct
>> for rotational lengthening
>> lincs_warnangle = 30 ; [degrees] maximum angle that a
>> bond can rotate before LINCS will complain
>>
>>
>> It is showing the following warning
>>
>> "For energy conservation with switch/shift potentials, rlist should be 0.1
>> to 0.3 nm larger than rvdw."
>>
>>
>>
>>
>>
>>
>> On Sun, May 12, 2013 at 11:57 PM, tarak karmakar <tarak20489 at gmail.com>
>> wrote:
>>>
>>> Oh !
>>> Thanks a lot Justin. I'll rerun all my jobs with this corrected mdp.
>>> Restrains things I didn't follow properly, anyway I'll read about this.
>>>
>>>
>>> On Sun, May 12, 2013 at 11:27 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>>
>>>> On 5/12/13 1:53 PM, tarak karmakar wrote:
>>>>>
>>>>> Thanks,
>>>>>
>>>>> I have used CGENFF force field parameters for the ligand generated from
>>>>> PARMCHEM with 0 penalties. For protein I have used CHARMM36 force
>>>>> field.
>>>>> my npt.mdp file is as follows,
>>>>>
>>>>> ; 7.3.3 Run Control
>>>>> integrator = md
>>>>
>>>>
>>>> Bug 1021 was only relevant with md-vv, so it is not your problem here.
>>>>
>>>>
>>>>> tinit = 0
>>>>> dt = 0.001
>>>>> nsteps = 5000000
>>>>> nstcomm = 1
>>>>> comm_grps = system
>>>>> comm_mode = linear
>>>>>
>>>>>
>>>>> ; 7.3.8 Output Control
>>>>> nstxout = 5000
>>>>> nstvout = 5000
>>>>> nstfout = 5000
>>>>> nstlog = 1000
>>>>> nstenergy = 1000
>>>>> nstxtcout = 1000
>>>>> xtc_precision = 1000
>>>>> xtc_grps = System
>>>>> energygrps = lIG Protein Water
>>>>>
>>>>> ; 7.3.9 Neighbor Searching
>>>>> nstlist = 10
>>>>> ns_type = grid
>>>>> pbc = xyz
>>>>> rlist = 1.2
>>>>>
>>>>> ; 7.3.10 Electrostatics
>>>>> coulombtype = PME
>>>>> rcoulomb = 1.2
>>>>>
>>>>> ; 7.3.11 VdW
>>>>> vdwtype = cut-off
>>>>> rvdw = 1.2
>>>>> DispCorr = EnerPres
>>>>>
>>>>
>>>> Your short-range settings are incorrect for strict use of CHARMM. You
>>>> should set:
>>>>
>>>> vdwtype = switch
>>>> rvdw-switch = 1.0
>>>> rlistlong = 1.4
>>>>
>>>> Your other settings for rlist, rcoulomb, and rvdw are fine.
>>>>
>>>>
>>>>> ; 7.3.13 Ewald
>>>>> fourierspacing = 0.12
>>>>> pme_order = 4
>>>>> ewald_rtol = 1e-5
>>>>>
>>>>> ; 7.3.14 Temperature Coupling
>>>>> tcoupl = nose-hoover
>>>>> tc_grps = system
>>>>> tau_t = 1.0
>>>>> ref_t = 300
>>>>>
>>>>> ; 7.3.15 Pressure Coupling
>>>>> pcoupl = parrinello-rahman
>>>>> pcoupltype = isotropic
>>>>> tau_p = 1.0
>>>>> compressibility = 4.5e-5
>>>>> ref_p = 1.0
>>>>>
>>>>> gen_vel = yes
>>>>
>>>>
>>>> In the absence of any restraints, initial velocity generation can
>>>> produce incorrect dynamics. This is why we use restraints. Thus far, your
>>>> observations simply seem consistent with random effects of improper
>>>> nonbonded parameters and/or equilibration.
>>>>
>>>> -Justin
>>>>
>>>>> gen_temp = 300
>>>>> gen_seed = 8877691
>>>>>
>>>>> ; 7.3.18 Bonds
>>>>> constraints = h-bonds
>>>>> constraint_algorithm = LINCS
>>>>> continuation = yes
>>>>> lincs_order = 4
>>>>> lincs_warnangle = 30
>>>>>
>>>>>
>>>>> On Sun, May 12, 2013 at 11:11 PM, Justin Lemkul <jalemkul at vt.edu>
>>>>> wrote:
>>>>>
>>>>>>
>>>>>>
>>>>>> On 5/12/13 1:34 PM, tarak karmakar wrote:
>>>>>>
>>>>>>> Thanks Justin for the Quick and Helpful reply.
>>>>>>>
>>>>>>> Yes. If I am right, the chaotic behavior of the simulations is
>>>>>>> inherent
>>>>>>> and can be assessed statistically by generating several independent
>>>>>>> trajectories and analyzing their similar outcomes. But with the same
>>>>>>> '.mdp'
>>>>>>> file I am getting TOO much different results, and that's where I
>>>>>>> worry.
>>>>>>> I'll surely try with the recent version of gromacs. But, for now, can
>>>>>>> you
>>>>>>> give me a little more informations about problems (bugs) with the
>>>>>>> 4.5.5
>>>>>>> version, related to my context?
>>>>>>>
>>>>>>>
>>>>>> The proposed relationship to bug 1012 is unclear to me. The issue
>>>>>> there
>>>>>> was an incompatibility between an integrator and thermostat, with
>>>>>> obvious
>>>>>> differences in thermodynamic output. Assessing your system in this
>>>>>> context
>>>>>> is not helpful. If you want to assess whether different core counts
>>>>>> or
>>>>>> hardware produce problems, then you need a very simple test case (like
>>>>>> a
>>>>>> box of water) that shows significant differences in averaged
>>>>>> observables.
>>>>>> As I said before, maybe your ligand parameters are insufficiently
>>>>>> accurate
>>>>>> (how did you generate them?) or .mdp settings are incorrect. Without
>>>>>> such
>>>>>> information, there is little point in trying to debug anything.
>>>>>>
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>> --
>>>>>> ==============================**==========
>>>>>>
>>>>>>
>>>>>> Justin A. Lemkul, Ph.D.
>>>>>> Research Scientist
>>>>>> Department of Biochemistry
>>>>>> Virginia Tech
>>>>>> Blacksburg, VA
>>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>>>
>>>>>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>>>>>
>>>>>> ==============================**==========
>>>>>>
>>>>>> --
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>>>>
>>>> --
>>>> ========================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Research Scientist
>>>> 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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