[gmx-users] Error during NVT equillibration with nvt.log file
ram bio
rmbio861 at gmail.com
Tue Oct 20 16:08:12 CEST 2009
Dear Justin,
Thanks.
I tried to equilibrate the system in NVT ensemble without constraints,
the equilibration completed, but the lipid layers moved apart, so i
tried to do simulated annealing procedure mentioned in the trouble
shooting section of the tutorial and here also i was able to
equilibrate only with the constraints = none option in anneal_npt.mdp
file (below).
title = Simulated Annealing
define = -DPOSRES -DPOSRES_LIPID
integrator = md
dt = 0.001
nsteps = 500000
continuation = no
constraints = none
constraint-algorithm = lincs
lincs-iter = 1
lincs-order = 4
nstxout = 1000
nstvout = 1000
nstfout = 1000
nstenergy = 1000
nstlist = 5
ns_type = grid
rlist = 1.2
rcoulomb = 1.2
rvdw = 1.2
coulombtype = PME
pme_order = 4
fourierspacing = 0.16
Tcoupl = Berendsen
tc_grps = Protein DPPC SOL_CL-
tau_t = 0.1 0.1 0.1
ref_t = 323 323 323
Pcoupl = Berendsen
Pcoupltype = semiisotropic
ref_p = 1.0 1.0
compressibility = 4.5e-5 4.5e-5
gen_vel = no
pbc = xyz
DispCorr = EnerPres
nstcomm = 1
comm-mode = Linear
comm-grps = Protein_DPPC SOL_CL-
annealing = single single single
annealing_npoints = 2 2 2
annealing_time = 0 500 0 500 0 500
annealing_temp = 0 323 0 323 0 323
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 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
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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
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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
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> Please search the archive at http://www.gromacs.org/search before posting!
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