[gmx-users] Error during NVT equillibration with nvt.log file
ram bio
rmbio861 at gmail.com
Tue Oct 27 15:28:47 CET 2009
Dear Justin,
Thanks for your patience and suggestions, as I am new to gromacs, i
had to confirm my results.
Ram
On Mon, Oct 26, 2009 at 4:28 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> ram bio wrote:
>>
>> Dear Justin,
>>
>> As per the suggestions, I have run NPT equillibration (without
>> constraints) for 1ns and observed the average values and plots in the
>> xmgrace as follows:
>>
>> 1) Pressure
>>
>> Energy Average RMSD Fluct. Drift
>> Tot-Drift
>>
>> -------------------------------------------------------------------------------
>> Pressure (bar) 0.967068 315.557 315.557 -0.00139934
>> -1.39934
>>
>> In the pressure.xvg plot the pressure was the same through out the
>> equilibration, that is no rise or fall in the graph, fluctuating in
>> the same range.
>>
>> 2) Density
>>
>> Energy Average RMSD Fluct. Drift
>> Tot-Drift
>>
>> -------------------------------------------------------------------------------
>> Density (SI) 1010.05 6.13912 4.17568 0.0155894
>> 15.5894
>>
>> In the density.xvg plot the density in the beginning was around 984
>> and then increased upto 500 ps then onwards was the same through out
>> the equilibration, that is no rise or fall in the graph, fluctuating
>> in the same range.
>>
>> 3) temperature
>>
>> Energy Average RMSD Fluct. Drift
>> Tot-Drift
>>
>> -------------------------------------------------------------------------------
>> Temperature 323 1.68979 1.68965 7.75704e-05
>> 0.0775705
>> Heat Capacity Cv: 12.4723 J/mol K (factor = 2.73692e-05)
>>
>> In the temperature.xvg plot the pressure was the same through out the
>> equilibration, that is no rise or fall in the graph, fluctuating in
>> the same range.
>>
>> 4) Box-x
>>
>> Statistics over 1000001 steps [ 0.0000 thru 1000.0001 ps ], 1 data sets
>> All averages are exact over 1000001 steps
>>
>> Energy Average RMSD Fluct. Drift
>> Tot-Drift
>>
>> -------------------------------------------------------------------------------
>> Box-X 6.81637 0.00919707 0.00692067 -2.09829e-05
>> -0.0209829
>>
>> In the box-x.xvg plot the value decreased from 6.82 - 6.84 to 6.79 -
>> 6.81 after the 500 ps and then was the same through out the
>> equilibration, that is no rise or fall in the graph, fluctuating in
>> the same range.
>>
>> 5) Box-Y the trend was same as X dimension
>>
>> Energy Average RMSD Fluct. Drift
>> Tot-Drift
>>
>> -------------------------------------------------------------------------------
>> Box-Y 6.84395 0.00923428 0.00694867 -2.10678e-05
>> -0.0210678
>>
>>
>> 5) Box-Z the trend was same as X dimension
>>
>> Statistics over 1000001 steps [ 0.0000 thru 1000.0001 ps ], 1 data sets
>> All averages are exact over 1000001 steps
>>
>> Energy Average RMSD Fluct. Drift
>> Tot-Drift
>>
>> -------------------------------------------------------------------------------
>> Box-Z 9.0932 0.0438719 0.036307 -8.53145e-05
>> -0.0853146
>>
>> In the box-z.xvg plot the value started from 9.3 and decreased to 9.03
>> at the 500 ps and then the values were fluctuating around this value
>> in the same run.
>>
>> Please suggest me are my equilibrated parameters ok for the MD
>> production run or i have to look for some more parameters and is it ok
>> if i run the production phase also without constraints and position
>> restraints.
>>
>
> You've presented six pieces of data that have all stabilized. You have to
> make the decision as to whether or not your equilibration is sufficient; you
> can't rely on others who know nothing about your project or its goals to
> continually check it and tell you if it's right.
>
> -Justin
>
>> The mdp file used for NPT is as below:
>>
>> title = NPT Equilibration
>> define = -DPOSRES
>> integrator = md
>> nsteps = 1000000
>> dt = 0.001
>> nstxout = 100
>> nstvout = 100
>> nstenergy = 100
>> nstlog = 100
>> continuation = yes
>> constraint_algorithm = lincs
>> constraints = none
>> lincs_iter = 1
>> lincs_order = 4
>> ns_type = grid
>> nstlist = 5
>> rlist = 1.2
>> rcoulomb = 1.2
>> rvdw = 1.2
>> coulombtype = PME
>> pme_order = 4
>> fourierspacing = 0.16
>> tcoupl = Nose-Hoover
>> tc-grps = Protein DPPC SOL_CL-
>> tau_t = 0.1 0.1 0.1
>> ref_t = 323 323 323
>> pcoupl = Parrinello-Rahman
>> pcoupltype = semiisotropic
>> tau_p = 5.0
>> ref_p = 1.0 1.0
>> compressibility = 4.5e-5 4.5e-5
>> pbc = xyz
>> DispCorr = EnerPres
>> gen_vel = no
>> nstcomm = 1
>> comm-mode = Linear
>> comm-grps = Protein_DPPC SOL_CL-
>>
>>
>> Thanks,
>>
>> 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
>>>>>>>>>> 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
>>>>>>>>> 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
>>>>>>> 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
>>>>> 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
>>> 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 posting!
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