[gmx-users] Inconsistent results in different clusters and cores

Sun May 12 20:27:21 CEST 2013

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>
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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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