[gmx-users] Error during NVT equillibration with nvt.log file
Justin A. Lemkul
jalemkul at vt.edu
Tue Oct 20 16:29:53 CEST 2009
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
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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
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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
========================================
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