<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial, helvetica, sans-serif;font-size:10pt;color:#000000;"><div>Hello,</div><div><br></div><div> I'm trying to turn off a Na+ charge using tpbconv in 4.5.4. There is only one Na+ counterion in my simulation. I create an index file, run tpbconv, and my output file looks like the following:</div><div><br></div><div>[mcharend@xanadu C4_IS]$ tpbconv -s md.tpr -o mdn.tpr -n index.ndx -zeroq</div><div><br></div><div>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span"
style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.</div><div><br></div><div><div>Reading toplogy and stuff from md.tpr</div><div>Reading file md.tpr, VERSION 4.5.4 (single precision)</div><div>500000 steps (1000 ps) remaining from first run.</div><div>Group 0 (
System) has 3037 elements</div><div>Group 1 ( Other) has 15 elements</div><div>Group 2 ( DRG) has 15 elements</div><div>Group 3 ( NA+) has 1 elements</div><div>Group 4 ( Water) has 3021 elements</div><div>Group 5 ( SOL) has 3021 elements</div><div>Group 6 ( non-Water) has 16 elements</div><div>Group 7 ( Ion) has 1 elements</div><div>Group 8 ( DRG) has 15 elements</div><div>Group 9 ( NA+) has
1 elements</div><div>Group 10 ( Water_and_ions) has 3022 elements</div><div>Group 11 ( NA+) has 1 elements</div><div>Select a group: 9</div><div>Selected 9: 'NA+'</div><div>Segmentation fault</div><div>[mcharend@xanadu C4_IS]$ </div></div><div><br></div><div>The bottom of my index.ndx file looks like:</div><div><br></div><div>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span"
style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span></div><div><br></div><div><div>[ NA+ ]</div><div>3037</div></div><div><br></div><div>Guidance appreciated. </div><div><br></div><div>Thanks , Marc</div><div style="position:fixed"></div>
</div></body></html>