[gmx-users] NVT with lipid bilayer
Dr Itamar Kass
ikass at uq.edu.au
Sat Dec 9 05:15:07 CET 2006
Justin Lemkul wrote:
> Hello all,
>
> I'm having a few more problems running an NVT ensemble on my system.
I have an
> integral membrane protein, with a transmembrane helix and small
extracellular
> domain. The bilayer is DPPC. I have one face of the bilayer solvated to
> surround the extracellular domain in water, and there are 3 sodium
counterions.
> I have successfully energy-minimized this system to a reasonable
potential
> energy (as mentioned previously on the list). I want to run short NVT
and NPT
> equilibration steps before running full-out MD simulations. I'm
having some
> trouble getting it started. I have attached my nvt.mdp file below,
along with
> an excerpt from my md.log file that highlights the problem. Is there
something
> obvious I'm missing? No matter what I try, the temperature and
pressure at Step
> 0 are always something extremely high.
>
> Thanks in advance, as always.
>
> -Justin
>
>
> Justin A. Lemkul
> Department of Biochemistry
> Virginia Tech
>
> (Running Gromacs 3.3 on Mac OS X 10.4.8; peptide parameters generated with
> Gromos96 FF, DPPC parameters from Tieleman)
>
> --------------------
> nvt.mdp
>
> title = NVT simulation
> cpp = /usr/bin/cpp
> include = -I../../../Topologies/
> constraints = all-bonds
> integrator = md
> dt = 0.002
> nsteps = 25000 ; 50 ps
> nstcomm = 1
> nstxout = 500
> nstvout = 0
> nstfout = 0
> nstlist = 5
> ns_type = grid
> rlist = 0.9
> coulombtype = cut-off
If you use coulombtype = cut-off, you do not need the fftw parameters.
> rcoulomb = 0.9
> rvdw = 1.4
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> optimize_fft = yes
> ; Berendsen temperature coupling is on in three groups
> Tcoupl = Berendsen
> tc-grps = Protein DPPC SOL_NA+
> tau_t = 0.1 0.1 0.1
> ref_t = 323 323 323
> ; Pressure coupling is not on
> Pcoupl = no
> pcoupltype = anisotropic
> tau_p = 2.0
> compressibility = 1.14e-4 1.14e-4 1.14e-4 0.0 0.0 0.0
> ref_p = 1.0 1.0 1.0 0.0 0.0 0.0
> ; Generate velocities is on - these are parameters from the tutorial
> gen_vel = yes
> gen_temp = 323
> gen_seed = 173529
>
>
> The output given by mdrun:
>
> Initializing LINear Constraint Solver
> number of constraints is 1331
> average number of constraints coupled to one constraint is 2.5
>
> Rel. Constraint Deviation: Max between atoms RMS
> Before LINCS 0.041987 701 702 0.009007
> After LINCS 0.000366 114 116 0.000053
>
>
> Constraining the coordinates at t0-dt (step -1)
> Rel. Constraint Deviation: Max between atoms RMS
> Before LINCS 0.092732 230 231 0.012284
> After LINCS 0.000116 114 116 0.000020
>
> Started mdrun on node 0 Thu Dec 7 20:29:26 2006
> Initial temperature: 324.422 K
> Step Time Lambda
> 0 0.00000 0.00000
>
> Grid: 9 x 13 x 9 cells
> Configuring nonbonded kernels...
> Testing Altivec/VMX support... present.
>
>
> Rel. Constraint Deviation: Max between atoms RMS
> Before LINCS 0.065170 1250 1251 0.004009
> After LINCS 0.000095 114 116 0.000016
>
> Energies (kJ/mol)
> Angle G96Angle Proper Dih. Ryckaert-Bell. Improper
Dih.
> 8.97802e+03 4.32995e+02 4.35659e+03 3.77124e+03
1.79014e+03
> LJ-14 Coulomb-14 LJ (SR) LJ (LR) Coulomb
(SR)
> 3.92013e+03 1.54916e+04 4.32277e+05 -3.48931e+03
-5.04310e+05
> Potential Kinetic En. Total Energy
Temperature
> Pressure (bar)
> -3.67824e+04 2.18253e+08 2.18216e+08 9.68265e+05
5.55747e+06
>
> Step 5, time 0.01 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> max 2.684103 (between atoms 345 and 346) rms 0.112125
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 335 337 36.0 0.1330 0.1681 0.1330
> 337 338 38.7 0.1000 0.1299 0.1000
> 337 339 89.0 0.1470 0.1627 0.1470
> 339 340 88.1 0.1530 0.1777 0.1530
> 340 342 32.9 0.1330 0.1681 0.1330
> 342 344 49.0 0.1470 0.1796 0.1470
> 344 345 54.9 0.1530 0.2429 0.1530
> 344 349 38.0 0.1530 0.1784 0.1530
> 345 346 90.0 0.1530 0.5637 0.1530
> 346 347 89.9 0.1530 0.4140 0.1530
> 346 348 90.0 0.1530 0.5249 0.1530
> Constraint error in algorithm Lincs at step 5
> Wrote pdb files with previous and current coordinates
>
> ***More LINCS errors***
>
> -------------------------------------------------------
> Program mdrun_3.3_gcc_mpi, VERSION 3.3
> Source code file: nsgrid.c, line: 226
>
> Range checking error:
> Explanation: During neighborsearching, we assign each particle to a grid
> based on its coordinates. If your system contains collisions or parameter
> errors that give particles very high velocities you might end up with some
> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
> put these on a grid, so this is usually where we detect those errors.
> Make sure your system is properly energy-minimized and that the potential
> energy seems reasonable before trying again.
>
> Variable ci has value -2147483648. It should have been within [ 0 ..
1053 ]
> Please report this to the mailing list (gmx-users at gromacs.org)
> -------------------------------------------------------
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This probably mean you have some problem with your start configuration.
Take a look at your starting system, there might be some collision
between atoms.
Good luck, Itamar.
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