Dear all,<div><br></div><div>I am trying to conduct some simple ligand binding studies for a protein system solvated in water. After inputting the command:</div><div><br></div><div>mdrun -v -deffnm em -nt 1 <br clear="all">
<div><br></div><div>I get the log shown below, nothing completes after this 0 step. Any help would be appreciated.</div><div><br></div><div><div>Back Off! I just backed up em.log to ./#em.log.14#</div><div>Getting Loaded...</div>
<div>Reading file em.tpr, VERSION 4.5.4 (single precision)</div><div>Loaded with Money</div><div><br></div><div><br></div><div>Back Off! I just backed up em.trr to ./#em.trr.3#</div><div><br></div><div>Back Off! I just backed up em.edr to ./#em.edr.3#</div>
<div><br></div><div>Steepest Descents:</div><div> Tolerance (Fmax) = 1.00000e+03</div><div> Number of steps = 50000</div><div>Warning: 1-4 interaction between 1 and 8 at distance 4.764 which is larger than the 1-4 table size 2.000 nm</div>
<div>These are ignored for the rest of the simulation</div><div>This usually means your system is exploding,</div><div>if not, you should increase table-extension in your mdp file</div><div>or with user tables increase the table size</div>
<div>mdrun -v -deffnm em -nt[1]+ Segmentation fault: 11 mdrun -v -deffnm em -nt 1</div><div>104-142:GLY lwollmuth$ tail -15 em.log</div><div>Configuring nonbonded kernels...</div><div>Configuring standard C nonbonded kernels...</div>
<div>Testing x86_64 SSE2 support... present.</div><div><br></div><div><br></div><div>Removing pbc first time</div><div><br></div><div>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++</div><div>S. Miyamoto and P. A. Kollman</div>
<div>SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid</div><div>Water Models</div><div>J. Comp. Chem. 13 (1992) pp. 952-962</div><div>-------- -------- --- Thank You --- -------- --------</div></div>
<div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div>The mdp input file is as below:</div><div><br></div><div><div>title<span class="Apple-tab-span" style="white-space:pre"> </span>= Minimization<span class="Apple-tab-span" style="white-space:pre"> </span>; Title of run</div>
<div><br></div><div>; Parameters describing what to do, when to stop and what to save</div><div>integrator<span class="Apple-tab-span" style="white-space:pre"> </span>= steep<span class="Apple-tab-span" style="white-space:pre"> </span>; Algorithm (steep = steepest descent minimization)</div>
<div>emtol<span class="Apple-tab-span" style="white-space:pre"> </span>= 1000.0 <span class="Apple-tab-span" style="white-space:pre"> </span>; Stop minimization when the maximum force < 10.0 kJ/mol</div><div>emstep <span class="Apple-tab-span" style="white-space:pre"> </span>= 0.01 <span class="Apple-tab-span" style="white-space:pre"> </span>; Energy step size</div>
<div>nsteps<span class="Apple-tab-span" style="white-space:pre"> </span>= 50000<span class="Apple-tab-span" style="white-space:pre"> </span> <span class="Apple-tab-span" style="white-space:pre"> </span>; Maximum number of (minimization) steps to perform</div>
<div>energygrps<span class="Apple-tab-span" style="white-space:pre"> </span>= Protein <span class="Apple-tab-span" style="white-space:pre"> </span>; Which energy group(s) to write to disk</div><div><br></div><div>; Parameters describing how to find the neighbors of each atom and how to calculate the interactions</div>
<div>nstlist<span class="Apple-tab-span" style="white-space:pre"> </span>= 1<span class="Apple-tab-span" style="white-space:pre"> </span> ; Frequency to update the neighbor list and long range forces</div><div>ns_type<span class="Apple-tab-span" style="white-space:pre"> </span>= grid<span class="Apple-tab-span" style="white-space:pre"> </span>; Method to determine neighbor list (simple, grid)</div>
<div>rlist<span class="Apple-tab-span" style="white-space:pre"> </span>= 1.0<span class="Apple-tab-span" style="white-space:pre"> </span>; Cut-off for making neighbor list (short range forces)</div><div>coulombtype<span class="Apple-tab-span" style="white-space:pre"> </span>= PME<span class="Apple-tab-span" style="white-space:pre"> </span>; Treatment of long range electrostatic interactions</div>
<div>rcoulomb<span class="Apple-tab-span" style="white-space:pre"> </span>= 1.0<span class="Apple-tab-span" style="white-space:pre"> </span>; long range electrostatic cut-off</div><div>rvdw<span class="Apple-tab-span" style="white-space:pre"> </span>= 1.0<span class="Apple-tab-span" style="white-space:pre"> </span>; long range Van der Waals cut-off</div>
<div>pbc<span class="Apple-tab-span" style="white-space:pre"> </span>= xyz <span class="Apple-tab-span" style="white-space:pre"> </span>; Periodic Boundary Conditions (yes/no)</div></div><div><br></div>-- <br>Rashek Kazi<br>
GS 2<br>MSTP Candidate<br>
</div>