[gmx-users] Error during NVT equillibration with nvt.log file
ram bio
rmbio861 at gmail.com
Tue Oct 20 16:54:36 CEST 2009
Dear Justin,
Thanks, will be back after some trials.
Ram
On Tue, Oct 20, 2009 at 8:16 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>>>>>>>>>> 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!
> 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
>
More information about the gromacs.org_gmx-users
mailing list