[gmx-users] mindist

[Sam David]

Hello gmx users

I'm calculating the minimum distance between solute and a surface at
different temperatures. The results I get are almost the same but density
profile and trajectory visualization show they are different.  I use
gmx mindist -f traj.xtc -s nvt.tpr  -n ind.ndx   -od distance.xvg  -b 40000

and I have tried different options in this command but all gave the same
distance. I made an index for two different atoms then calculated the
distance for both of them to the surface but the distances were the same
for both of them where it should be different because these atoms are from
different part from the solute

Any ideas or suggestions?

Thank you