[gmx-users] tpbconv question
tsjerkw at gmail.com
Fri Sep 30 06:29:26 CEST 2011
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
On Sep 30, 2011 3:05 AM, "Marc Charendoff" <mcharend at sbcglobal.net> wrote:
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+'
[mcharend at xanadu C4_IS]$
The bottom of my index.ndx file looks like:
. . . . . . . . . . . . . . . . .
[ NA+ ]
Thanks , Marc
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