<div>dear teacher,</div><div>when i do remd in the npt ensemble.</div><div><br></div><div>=========md.mdp===================</div><div>; Start time and timestep in ps</div><div>tinit = 0</div><div>dt = 0.000001</div>
<div>nsteps = 50000000</div><div>; For exact run continuation or redoing part of a run</div><div><br></div><div>; Temperature coupling</div><div>Tcoupl = nose-hoover</div><div>; Groups to couple separately</div>
<div>tc_grps = system</div><div>; Time constant (ps) and reference temperature (K)</div><div>tau_t = 0.3</div><div>ref_t = 800</div><div>; Pressure coupling</div><div>
Pcoupl = berendsen</div><div>pcoupltype = isotropic</div><div>; Time constant (ps), compressibility (1/bar) and reference P (bar)</div><div>tau_p = 0.5</div><div>compressibility = 6.5e-5</div>
<div>ref_p = 1.0</div><div>==========error========================</div><div>step 999900, will finish Mon Nov 28 00:11:22 2011</div><div>step 1000000, will finish Mon Nov 28 00:11:19 2011</div><div><br>
</div><div>Step 1000002 Warning: pressure scaling more than 1%, mu: 333821 333821 333821</div><div><br></div><div>Step 1000002 Warning: pressure scaling more than 1%, mu: 455440 455440 455440</div><div><br></div><div>-------------------------------------------------------</div>
<div>Program mdrun_mpi_4.5.5, VERSION 4.5.5</div><div>Source code file: smalloc.c, line: 214</div><div><br></div><div>Fatal error:</div><div>Not enough memory. Failed to realloc -5476105916 bytes for grid->nra, grid->nra=0x38ce0</div>
<div>(called from file nsgrid.c, line 483)</div><div>For more information and tips for troubleshooting, please check the GROMACS</div><div>website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a></div>
<div>-------------------------------------------------------</div><div>===============command=====================</div><div>mpirun n8,8,8,11,11,11,11,2 -np $n_thread /export/software/bin/mdrun_mpi_4.5.5 -multidir ./0/ ./1/ ./2/ ./3/ ./4/ ./5/ ./6/ ./7/ ./8/ ./9/ ./10/ ./11/ ./12/ ./13/ ./14/ ./15/ -replex 500000 -nice 0 -s pmma.tpr -o md -c after_md -pd -v >& log1 &</div>
<div><br></div><div>how could i do except use the smaller dt or big/small tau_p ?</div><div><br></div><div>thanks!</div><div>bodu </div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 14px; border-collapse: collapse; color: rgb(80, 0, 80); "> Bo Du<br>
Department of Polymer Science and Engineering,<br> School of Chemical Engineering and technology,<br>Tianjin University, Weijin Road 92, Nankai District 300072,<br>Tianjin City P. R. China<br> Tel/Fax: +86-22-27404303<br>
E-mail: <a href="mailto:2008dubo@gmail.com" style="color: rgb(17, 85, 204); ">2008dubo@gmail.com</a><br></span></div>