[gmx-users] Error during NVT equillibration with nvt.log file

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 20 16:10:17 CEST 2009 


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
>>>>> _______________________________________________
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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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>> --
>> ========================================
>>
>> 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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> 

-- 
========================================

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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