[gmx-users] NVT with lipid bilayer

[Justin Lemkul]

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
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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