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@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 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. _______________________________________________ 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