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

[Justin A. Lemkul]

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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