Hi, everyone<br><br>I used a double precision version of gromacs, to simulate a SiO2 on a DPPC bilayer.<br>And here is my md.mdp. I have not add pull code into it.<br><br>title = fws<br>cpp = /usr/bin/cpp<br>
constraints = all-bonds<br>constraint_algorithm= SHAKE<br>integrator = md<br>dt = 0.002 ; ps !<br>nsteps = 50000 ; total 100 ps.<br>nstcomm = 1<br>nstxout = 500<br>
nstvout = 0<br>nstfout = 0<br>nstlist = 10<br>ns_type = grid<br>rlist = 1.0<br>coulombtype = PME<br>rcoulomb = 1.0<br>vdwtype = cut-off<br>
rvdw = 1.4<br>fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 6<br>ewald_rtol = 1e-5<br>
optimize_fft = yes<br>; Berendsen temperature coupling is on in three groups<br>Tcoupl = berendsen<br>tc_grps = System<br>tau_t = 0.1<br>ref_t = 300<br>
; Pressure coupling is on<br>Pcoupl = parrinello-rahman<br>pcoupltype = isotropic<br>tau_p = 1.0<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>; Generate velocites is on at 300 K.<br>
gen_vel = yes<br>gen_temp = 300.0<br>gen_seed = 173529<br><br>and command line<br><br>gromppd -f md.mdp -c dppc128_pull.gro -p em.top -o dppc128_pull.tpr -maxwarn 1 -n pull.ndx<br><br>
NOTE 1 [file md.mdp, line unknown]:<br> The Berendsen thermostat does not generate the correct kinetic energy<br> distribution. You might want to consider using the V-rescale thermostat.<br><br>NOTE 2 [file em.top, line unknown]:<br>
The largest charge group contains 25 atoms.<br> Since atoms only see each other when the centers of geometry of the charge<br> groups they belong to are within the cut-off distance, too large charge<br> groups can lead to serious cut-off artifacts.<br>
For efficiency and accuracy, charge group should consist of a few atoms.<br> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.<br><br><br>mdrund -s dppc128_pull.tpr -v<br><br>and here is the output<br>
...<br>step 100, will finish Mon Mar 29 00:25:14 2010<br>step 200, will finish Mon Mar 29 00:26:05 2010<br>step 300, will finish Mon Mar 29 00:23:37 2010<br>step 400, will finish Mon Mar 29 00:22:22 2010<br>Inner product between old and new vector <= 0.0!<br>
constraint #96 atoms 17442 and 17453<br>Wrote pdb files with previous and current coordinates<br>Inner product between old and new vector <= 0.0!<br>constraint #14 atoms 17375 and 17392<br>Wrote pdb files with previous and current coordinates<br>
Inner product between old and new vector <= 0.0!<br>constraint #13 atoms 17374 and 17392<br><br>t = 0.930 ps: Water molecule starting at atom 24890 can not be settled.<br>Check for bad contacts and/or reduce the timestep.<br>
Wrote pdb files with previous and current coordinates<br>Segmentation fault<br><br><br clear="all"><br>Di Cheng<br><br>University of Science and Technology of China<br>Hefei, Anhui Province 230026<br>P. R. China<br>E-mail: <a href="mailto:chengdi@mail.ustc.edu.cn">chengdi@mail.ustc.edu.cn</a><br>
Tel.: +86-15321055911<br><br>