[gmx-users] System blowing up in final MD run
Deep Bhattacharya
hypergenetics at gmail.com
Wed Jul 13 14:56:33 CEST 2016
Hello Tsjerk,
These are the notes that I got before running the NPT equilibration
NOTE 1 [file npt.mdp]:
leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
Generated 165 of the 1596 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'UNK'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'NA'
The center of mass of the position restraint coord's is 3.516 4.410 3.815
NOTE 2 [file topol.top]:
The largest charge group contains 11 atoms.
Since atoms only see each other when the centers of geometry of the charge
groups they belong to are within the cut-off distance, too large charge
groups can lead to serious cut-off artifacts.
For efficiency and accuracy, charge group should consist of a few atoms.
For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
NOTE 3 [file topol.top]:
The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has
an estimated oscillational period of 1.0e-02 ps, which is less than 10
times the time step of 1.0e-03 ps.
Maybe you forgot to change the constraints mdp option.
Number of degrees of freedom in T-Coupling group Protein_UNK is 5339.83
Number of degrees of freedom in T-Coupling group Water_and_ions is 89787.17
NOTE 4 [file npt.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
I am using GROMOS53a6 forcefield. The system is a protein carbohydrate
solvent system. While observing the trajectory during the MD run, I found
that the system was blowing up.
Please help.
Sincerely,
Deep Bhattacharya
On Wed, Jul 13, 2016 at 12:37 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
wrote:
> Hi Deep,
>
> What force field? What system? How many cores? Did you try running on one?
> What error? Did pdb2gmx or grompp give any warnings?
>
> Cheers,
>
> Tsjerk
>
> On Wed, Jul 13, 2016 at 5:44 AM, Deep Bhattacharya <
> hypergenetics at gmail.com>
> wrote:
>
> > Hello,
> > My system is blowing up for the protein carbohydrate solvent complex. I
> > have attached the mdp file below. The NPT and NVT were in good accordance
> > to tutorial listed by Justin. 'Please help me solve the issue.
> > title = CD44 complex MD simulation
> > ; Run parameters
> > integrator = md ; leap-frog integrator
> > nsteps = 10000000 ; 0.001 * 1000000 = 10000 ps (10 ns)
> > dt = 0.001 ; 1 fs
> > ; Output control
> > nstxout = 50000 ; suppress .trr output
> > nstvout = 50000 ; suppress .trr output
> > nstenergy = 50000 ; save energies every 1000.0 ps
> > nstlog = 50000 ; update log file every 1000.0 ps
> > nstxtcout = 50000
> > xtc_precision = 1000
> > energygrps = Protein LIG SOL
> > ; Bond parameters
> > continuation = yes ; first dynamics run
> > constraint_algorithm = lincs ; holonomic constraints
> > constraints = all-bonds ; all bonds (even heavy atom-H bonds)
> > constrained
> > lincs_iter = 1 ; accuracy of LINCS
> > lincs_order = 4 ; also related to accuracy
> > ; Neighborsearching
> > ns_type = grid ; search neighboring grid cells
> > nstlist = 1 ;
> > rcoulomb = 0.81
> > rvdw = 0.81
> > coulombtype = Cut-off ; Particle Mesh Ewald for long-
> > vdwtype = cut-off
> > rlistlong = 1.4
> > epsilon-rf = 61
> > rlist = 0.8
> > ; Temperature coupling is on
> > tcoupl = nose-hoover ; modified Berendsen thermostat
> > tc-grps =Protein_LIG Water_and_ions ; two coupling groups - more
> > accurate
> > tau_t = 2.0 2.0 ; time constant, in ps
> > ref_t = 300 300 ; reference temperature, one for each group, in K
> > ; Pressure coupling is on
> > pcoupl = Parrinello-Rahman ; Pressure coupling on in
> NPT
> > pcoupltype = isotropic ; uniform scaling of box vectors
> > tau_p = 6.0 ; time constant, in ps
> > ref_p = 1.0 ; reference pressure, in bar
> > compressibility = 4.5e-5 ; isothermal compressibility of
> > water, bar^-1
> > refcoord_scaling = com
> > ; Periodic boundary conditions
> > pbc = xyz ; 3-D PBC
> > ; Dispersion correction
> > DispCorr = EnerPres ; account for cut-off vdW scheme
> > ; Velocity generation
> > gen_vel = no ; assign velocities from Maxwell distribution
> >
> >
> > Steepest Descents converged to Fmax < 1000 in 573 steps
> > Potential Energy = -7.58370311664555e+05
> > Maximum force = 9.53896348096555e+02 on atom 1163
> > Norm of force = 2.44608995242254e+01
> >
> >
> > *Deep S Bhattacharya*
> >
> > *Graduate Research Assistant*
> >
> > Mohs Biomedical Imaging & Nanotechnology Group
> >
> > Pharmaceutical Sciences
> >
> > *University of Nebraska Medical Center*
> >
> > 4018 Eppley Science Hall | Omaha, NE 68198-6805
> >
> > office 402.559.4349 | cell 402.906.1640
> >
> > deep.bhattacharya at unmc.edu.deep.bhattacharya199@gmail.com
> > --
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
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--
Deep Bhattacharya.
Post-Graduate Student,
Department of Pharmaceutical Chemistry,
Bombay College Of Pharmacy.
Mobile - +918976129616
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