Dear gmx-users, <br><br>I run MD for a protein molecule solvated with water molecules. <br>Until now it works well, however strangely they started to crash, I don't know the reason. <br>So, if anyone have similar problem please let me know the solution. <br>
It seems like that NPT system might cause some problems. <br><br>Also, when I continue MD further, it works.<br>(Sometimes simulation crashes after 1 ns, but sometimes it crashes only after 100 ps.) <br>Then, can I use those results for further studies? <br>
<br>This is the mdp file: <br><div style="margin-left: 40px;">integrator = md<br>nsteps = 1500000 <br>dt = 0.002 <br>nstlist = 10 <br>rlist = 1.0<br>coulombtype = pme <br>rcoulomb = 1.0 <br>vdw-type = cut-off <br>
rvdw = 1.0<br>tcoupl = Berendsen<br>tc-grps = protein non-protein<br>tau-t = 0.1 0.1 <br>ref-t = 310 310 <br>pcoupl = Berendsen <br>pcoupltype = isotropic<br>tau-p = 1<br>ref-p = 1.0<br>
compressibility = 4.5e-5<br>constraints = all-bonds <br>constraint_algorithm = lincs <br>nstxout = 1000 <br>nstvout = 10000 <br>nstxtcout = 100 <br>nstenergy = 100 <br>; Generate velocity is on at 300 K <br>
gen_vel = yes <br>gen_temp = 300.0 <br>gen_seed = 173529<br></div><br>This is the error message: <br><div style="margin-left: 40px;">-------------------------------------------------------<br>Program mdrun_mpi_d, VERSION 3.3.1<br>
Source code file: nsgrid.c, line: 226<br> <br>Range checking error:<br>Explanation: During neighborsearching, we assign each particle to a grid<br>based on its coordinates. If your system contains collisions or parameter<br>
errors that give particles very high velocities you might end up with some<br>coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot<br>put these on a grid, so this is usually where we detect those errors. <br>
Make sure your system is properly energy-minimized and that the potential<br>energy seems reasonable before trying again.<br> <br>Variable ci has value 3185. It should have been within [ 0 .. 3072 ]<br>Please report this to the mailing list (<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>)<br>
-------------------------------------------------------<br> <br>"Interfacing Space and Beyond..." (P. J. Harvey) <br> <br>Error on node 1, will try to stop all the nodes<br>Halting parallel program mdrun_mpi_d on CPU 1 out of 16<br>
<br>gcq#307: "Interfacing Space and Beyond..." (P. J. Harvey) <br> <br>[1] MPI Abort by user Aborting program !<br>[1] Aborting program!<br>-------------------------------------------------------<br></div>-- <br>
--------------------------------------------------<br>'God used beautiful mathematics in creating the world.'<br>-Paul Dirac <br>'But he created too many objects.'<br>-Seungpyo Hong <br><br>Seungpyo Hong <br>
Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea<br>Tel. (82)-18-372-2468<br><a href="mailto:sphong_@kaist.ac.kr">sphong_@kaist.ac.kr</a><br><a href="mailto:sp1020@gmail.com">sp1020@gmail.com</a>