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

[Justin A. Lemkul]

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

========================================