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

[tarak karmakar]

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
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

; 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
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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