[gmx-users] Error during NVT equillibration with nvt.log file
Justin A. Lemkul
jalemkul at vt.edu
Tue Oct 20 16:46:03 CEST 2009
ram bio wrote:
> 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)..
>
Yes, normal NPT.
-Justin
> 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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>>>>>>>>> posting!
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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
>>>>>>
>>>>>> ========================================
>>>>>> _______________________________________________
>>>>>> 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
>>>>>> posting!
>>>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>>>> interface
>>>>>> or send it to gmx-users-request at gromacs.org.
>>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>>
>>>> --
>>>> ========================================
>>>>
>>>> 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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>>>> or send it to gmx-users-request 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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