[gmx-users] Error during NVT equillibration with nvt.log file

ram bio rmbio861 at gmail.com
Tue Oct 20 16:42:40 CEST 2009


Dear Justin,

Thanks for the advice and suggestions,  will look into the plots and
try to run a further NPT equillibration, (here you mean equilibration
phase 2 ? without annealing, as in the tutorial)..

Please let me know.

Ram

On Tue, Oct 20, 2009 at 7:59 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> ram bio wrote:
>>
>> Dear Justion,
>>
>> When I executed the command g_energy -f anneal_npt1.edr, the output
>> for temperature and pressure were as under:
>>
>> Statistics over 500001 steps [ 0.0000 thru 500.0000 ps ], 1 data sets
>> All averages are exact over 500001 steps
>>
>> Energy                      Average       RMSD     Fluct.      Drift
>>  Tot-Drift
>>
>> -------------------------------------------------------------------------------
>> Temperature                  161.41    93.1199          0   0.645591
>>  322.796
>> Heat Capacity Cv:       24.906 J/mol K (factor = 0.332832)
>>
>> Statistics over 500001 steps [ 0.0000 thru 500.0000 ps ], 1 data sets
>> All averages are exact over 500001 steps
>>
>> Energy                      Average       RMSD     Fluct.      Drift
>>  Tot-Drift
>>
>> -------------------------------------------------------------------------------
>> Pressure (bar)             -7.96937    115.169    114.406  0.0916656
>>  45.8329
>>
>> i am unable to understand from these parameters, whether the system is
>> ok for future steps.
>
> Because simply looking at averages is less useful than looking at the plots.
>  I asked whether the temperature had stabilized, not what it's average value
> was. Consider this - you're constantly increasing the temperature, so an
> average is useless.  Look at the plot that g_energy gives you and make sure
> the increase is as you would expect.  Probably a further NPT equilibration
> is needed to make sure that the temperature will remain stable without the
> influence of annealing.
>
> Same thing for pressure - look at the plot.  Wide fluctuations will occur,
> so that's not a problem.  The trend is what is important (i.e., running
> average in xmgrace).  Is the pressure leveling off?  The average is more
> meaningful here, and it looks a bit low, but as I advise in my tutorial,
> equilibrating membrane systems takes a *long* time, anyway.
>
> -Justin
>
>> Regarding the gaps in the lipid bilayers,now when i visualized the
>> .trr file in the VMD there were no gaps in the lipid bilayer, that is
>> they did not move apart.
>>
>> Please help.
>>
>> Thanks
>>
>> Ram
>>
>>
>>
>>
>>
>>
>> On Tue, Oct 20, 2009 at 7:40 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>>
>>> ram bio wrote:
>>>
>>> <snip>
>>>
>>>> Now as i would like to proceed further, please suggest me how to
>>>> confirm that the simulated annealing was proper and also please let me
>>>> know can i now go to npt equillibration using the output of simulated
>>>> annealing as input to npt equilibration.
>>>>
>>> Like you would anything else.  Have the temperature and pressure
>>> stabilized?
>>>  Is your structure reasonable (no gaps, etc)?
>>>
>>> -Justin
>>>
>>>> Like I am going to use the following command to run the npt
>>>> equillibration:
>>>>
>>>> grompp -f npt.mdp -c anneal_npt1.gro -t anneal_npt.trr -p topol.top -n
>>>> index.ndx -o npt.tpr
>>>>
>>>> Thanks,
>>>>
>>>> Ram
>>>>
>>>>
>>>>
>>>>
>>>> On Fri, Oct 16, 2009 at 10:14 PM, Justin A. Lemkul <jalemkul at vt.edu>
>>>> wrote:
>>>>>
>>>>> ram bio wrote:
>>>>>>
>>>>>> Dear Justin,
>>>>>>
>>>>>> Thanks and I tried your suggestion, that is minimizing the system
>>>>>> without restraints and increasing the Fmax to 1000, the mdp file used
>>>>>> is as follows:
>>>>>>
>>>>> Note that I only suggested EM, not necessarily Fmax < 1000.  You
>>>>> original
>>>>> post contained an even lower Fmax, suggesting that you can do better
>>>>> than
>>>>> 1000.  The parameters in my tutorial are somewhat generic; you should
>>>>> alter
>>>>> them to suit your needs.
>>>>>
>>>>> <snip>
>>>>>
>>>>> Please note that the headers of log files are typically unnecessary
>>>>> when
>>>>> posting the .mdp file.
>>>>>
>>>>>> please suggest me is it ok to remove the constraints and run the NVT
>>>>>> equillibration.
>>>>>>
>>>>> You can try it, but I doubt it will make a difference.  Your simulation
>>>>> is
>>>>> crashing before it is even starting, making it very difficult to
>>>>> diagnose.
>>>>>  You probably need to re-build the system, using as rigorous criteria
>>>>> as
>>>>> possible during the InflateGRO steps to ensure that you don't have any
>>>>> improper atomic overlap.  In my experience, if the simulation is
>>>>> failing
>>>>> at
>>>>> step 0, there is no hope for coaxing the system into working.  The
>>>>> configuration simply isn't reasonable.
>>>>>
>>>>> -Justin
>>>>>
>>>>>> Thanks
>>>>>>
>>>>>> Ram
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Fri, Oct 16, 2009 at 9:27 PM, Justin A. Lemkul <jalemkul at vt.edu>
>>>>>> wrote:
>>>>>>>
>>>>>>> ram bio wrote:
>>>>>>>>
>>>>>>>> Dear Gromacs users,
>>>>>>>>
>>>>>>>> I am doing protein in lipid-bilayer simulation and i am following
>>>>>>>> the
>>>>>>>> procedure as per justin tutorial. I am able to insert the protein in
>>>>>>>> lipid bilayer and minimize the system as per Inflategro
>>>>>>>> procedure,during the total procedure the system was minimized in
>>>>>>>> every
>>>>>>>> step.Then, I solvated and ionized sytem and minimized using the
>>>>>>>> following mdp file:
>>>>>>>>
>>>>>>>> ; minim.mdp - used as input into grompp to generate em.tpr
>>>>>>>> ; Parameters describing what to do, when to stop and what to save
>>>>>>>> define = -DSTRONG_POSRES
>>>>>>>> integrator      = steep         ; Algorithm (steep = steepest
>>>>>>>> descent
>>>>>>>> minimization)
>>>>>>>> emtol           = 500.0         ; Stop minimization when the maximum
>>>>>>>> force < 1000.0 kJ/mol/nm
>>>>>>>> emstep          = 0.01          ; Energy step size
>>>>>>>> nsteps          = 50000         ; Maximum number of (minimization)
>>>>>>>> steps to perform
>>>>>>>>
>>>>>>>> ; Parameters describing how to find the neighbors of each atom and
>>>>>>>> how
>>>>>>>> to calculate the interactions
>>>>>>>> nstlist         = 1             ; Frequency to update the neighbor
>>>>>>>> list and long range forces
>>>>>>>> ns_type         = grid          ; Method to determine neighbor list
>>>>>>>> (simple, grid)
>>>>>>>> rlist           = 1.2           ; Cut-off for making neighbor list
>>>>>>>> (short range forces)
>>>>>>>> coulombtype     = PME           ; Treatment of long range
>>>>>>>> electrostatic interactions
>>>>>>>> rcoulomb        = 1.2           ; Short-range electrostatic cut-off
>>>>>>>> rvdw            = 1.2           ; Short-range Van der Waals cut-off
>>>>>>>> pbc             = xyz           ; Periodic Boundary Conditions
>>>>>>>> (yes/no)
>>>>>>>>
>>>>>>>> the output was as follows:
>>>>>>>>
>>>>>>>> Steepest Descents converged to Fmax < 500 in 4770 steps
>>>>>>>> Potential Energy  = -3.8820288e+05
>>>>>>>> Maximum force     =  4.4803549e+02 on atom 3573
>>>>>>>> Norm of force     =  1.7854408e+01
>>>>>>>>
>>>>>>>> As the potential energy and Fmax values were agreeable , I proceeded
>>>>>>>> to equillibrate the system using NVT.
>>>>>>>>
>>>>>>> Did you minimize the structure without restraints, prior to NVT?
>>>>>>>
>>>>>>> <snip>
>>>>>>>
>>>>>>>>       Angle       G96Angle    Proper Dih. Ryckaert-Bell.  Improper
>>>>>>>> Dih.
>>>>>>>>  2.20077e+04    8.54042e+03    6.78950e+03    4.34650e+03
>>>>>>>>  3.03266e+03
>>>>>>>>       LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb
>>>>>>>> (SR)
>>>>>>>>  4.76527e+03    5.50236e+04    8.36617e+06   -2.20019e+03
>>>>>>>> -4.46844e+05
>>>>>>>>  Coul. recip. Position Rest.      Potential    Kinetic En.   Total
>>>>>>>> Energy
>>>>>>>>  -1.65524e+05    1.07769e+01    7.85612e+06    5.88813e+10
>>>>>>>>  5.88892e+10
>>>>>>>>  Conserved En.    Temperature Pressure (bar)  Cons. rmsd ()
>>>>>>>>  5.88892e+10    2.23805e+08    1.21713e+09    3.10245e+01
>>>>>>>>
>>>>>>> In my experience, the combination of an astronomically high
>>>>>>> temperature
>>>>>>> and
>>>>>>> a repulsive temperature is indicative of restraining an
>>>>>>> unrestrainable
>>>>>>> starting structure.  Try the EM I suggested above.  Other than that,
>>>>>>> as
>>>>>>> I've
>>>>>>> suggested before, see the Advanced Troubleshooting page I created in
>>>>>>> the
>>>>>>> tutorial.
>>>>>>>
>>>>>>> -Justin
>>>>>>>
>>>>>>>> Please help me to proceed further and let me know where are the
>>>>>>>> mistakes lying and how to overcome them.
>>>>>>>>
>>>>>>>> Thanks in advance,
>>>>>>>>
>>>>>>>> Ram
>>>>>>>> _______________________________________________
>>>>>>>> gmx-users mailing list    gmx-users at gromacs.org
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>>>>>>>>
>>>>>>> --
>>>>>>> ========================================
>>>>>>>
>>>>>>> Justin A. Lemkul
>>>>>>> Ph.D. Candidate
>>>>>>> ICTAS Doctoral Scholar
>>>>>>> Department of Biochemistry
>>>>>>> Virginia Tech
>>>>>>> Blacksburg, VA
>>>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>>>>
>>>>>>> ========================================
>>>>>>> _______________________________________________
>>>>>>> gmx-users mailing list    gmx-users at gromacs.org
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>>>>>>>
>>>>> --
>>>>> ========================================
>>>>>
>>>>> Justin A. Lemkul
>>>>> Ph.D. Candidate
>>>>> ICTAS Doctoral Scholar
>>>>> Department of Biochemistry
>>>>> Virginia Tech
>>>>> Blacksburg, VA
>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>>
>>>>> ========================================
>>>>> _______________________________________________
>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> Please search the archive at http://www.gromacs.org/search before
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>>>>>
>>> --
>>> ========================================
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
>>> _______________________________________________
>>> gmx-users mailing list    gmx-users at gromacs.org
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>>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
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