[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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