Hello,
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:
[mcharend@xanadu C4_IS]$ tpbconv -s md.tpr -o mdn.tpr -n index.ndx -zeroq
...................
Reading toplogy and stuff from md.tpr
Reading file md.tpr, VERSION 4.5.4 (single precision)
500000 steps (1000 ps) remaining from first run.
Group 0 ( System) has 3037 elements
Group 1 ( Other) has 15 elements
Group 2 ( DRG) has 15 elements
Group 3 ( NA+) has 1 elements
Group 4 ( Water) has 3021 elements
Group 5 ( SOL) has 3021 elements
Group 6 ( non-Water) has 16 elements
Group 7 ( Ion) has 1 elements
Group 8 ( DRG) has 15 elements
Group 9 ( NA+) has 1 elements
Group 10 ( Water_and_ions) has 3022 elements
Group 11 ( NA+) has 1 elements
Select a group: 9
Selected 9: 'NA+'
Segmentation fault
[mcharend@xanadu C4_IS]$
The bottom of my index.ndx file looks like:
.................
[ NA+ ]
3037
Guidance appreciated.
Thanks , Marc
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