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@gromacs.org) ------------------------------------------------------- _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php