[gmx-users] Re:g_mindist option

[alkasrivastava at iitb.ac.in]

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