[gmx-users] Inconsistent results in different clusters and cores
tarak karmakar
tarak20489 at gmail.com
Fri May 17 10:04:34 CEST 2013
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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