[gmx-users] tpbconv question

[Tsjerk Wassenaar]

Hi Marc,

I think that -zeroq ignores the indexing. Using an index will extract a .tpr
for the index group only, which is not what you want. There is no simple way
to do what you want (using tpbconv). You'll have to modify the charge in the
.top file and generate a new .tpr

Cheers,

Tsjerk

On Sep 30, 2011 3:05 AM, "Marc Charendoff" <mcharend at sbcglobal.net> wrote:

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 at 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 at xanadu C4_IS]$

The bottom of my index.ndx file looks like:

. . . . . . . . . . . . . . . . .

[ NA+ ]
3037

Guidance appreciated.

Thanks , Marc

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