[gmx-users] Inconsistent results in different clusters and cores
tarak karmakar
tarak20489 at gmail.com
Fri May 17 10:16:13 CEST 2013
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://vt.edu/Pages/Personal/justin>
>>>>> <h**ttp://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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>>
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