Hi
I am doing a 5 peptide simulation in a 6nm box. Now to check the
correctness of my simulation i m calculating the minimum periodic distance
using g_mindist to find out the distance between molecule and its periodic
images.Following is the command i have used
g_mindist -s full.tpr -f full.xtc -n index.ndx -pi -od mindist.xvg
For the selection criteria i have used c-alpha atom of peptide 1. It is
giving me the minimum distance of 6nm as expected but how can i see the
maximum distance because by applying -max option also i am getting the
same result
1. g_mindist -s full.tpr -f full.xtc -n index.ndx -pi -od mindist.xvg
Select a group: 19
Selected 19: 'c-alpha-gly1'
Reading frame 16600 time 8300.000
The shortest periodic distance is 6 (nm) at time 0 (ps)
this is the part of output mindist.xvg
0 6.000 0.000 6.000 6.000 6.000
0.5 6.000 0.000 6.000 6.000 6.000
1 6.000 0.000 6.000 6.000 6.000
1.5 6.000 0.000 6.000 6.000 6.000
2 6.000 0.000 6.000 6.000 6.000
2.5 6.000 0.000 6.000 6.000 6.000
3 6.000 0.000 6.000 6.000 6.000
2. g_mindist -s full.tpr -f full.xtc -n index.ndx -pi -od mindist.xvg -max
Select a group: 19
Selected 19: 'c-alpha-gly1'
Reading frame 16610 time 8300.000
The shortest periodic distance is 6 (nm) at time 0 (ps)
The part of output mindist.xvg
0 6.000 0.000 6.000 6.000 6.000
0.5 6.000 0.000 6.000 6.000 6.000
1 6.000 0.000 6.000 6.000 6.000
1.5 6.000 0.000 6.000 6.000 6.000
2 6.000 0.000 6.000 6.000 6.000
2.5 6.000 0.000 6.000 6.000 6.000
3 6.000 0.000 6.000 6.000 6.000
The minimum distance is 6nm and it is exactly what is expected but there
should also be distances more than 6nm (considering 26 periodic images). I
don't know how to get that. Also i want to ask one more thing what is
"maximum internal distance " which is probably indicated by the third
column of mindist.xvg output.
Thanks
Regards
Alka
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