[gmx-users] Error during NVT equillibration with nvt.log file
ram bio
rmbio861 at gmail.com
Tue Oct 20 16:25:25 CEST 2009
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.
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
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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
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>>> 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
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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