Hi, I am trying to calculate the distance between two atoms, which are defined in an index file. The command that I use is:
"gmx distance -f output.gro -s prod.tpr -n index.ndx -oav distance.xvg"
I get the obvious:
"Selection 'atom_name' does not evaluate into an even number of positions (there are 1 positions)"
The same happens if I use in -f prod.trr
What might be wrong? Any insights on what to look for? What usually gives this kind of error?
Feel free to ask for any further information.
Thanks in advance
Thanks Nik, the answer was actually in the manual. When you are prompted for an option you have to specify a pair.
If you were used to g_dist, you can read in the page of Gromacs that in 5.0 the tool 'gmx distance' has a variation respect g_dist:
"g_dist
This tool has been removed in 5.0. A replacement is gmx distance (for most options) or gmx select (for -dist or -lt).
If you had index groups A and B in index.ndx for g_dist, you can use the following command to compute the same distance with gmx distance:
gmx distance -n index.ndx -select 'com of group "A" plus com of group "B"' -oxyz -oall
The -intra switch is replaced with -nopbc.
If you used -dist D, you can do the same calculation with gmx select:
gmx select -n index.ndx -select 'group "B" and within D of com of group "A"' -on/-oi/-os/-olt
You can select the output option that best suits your post-processing needs (-olt is a replacement for g_dist -dist -lt)"
http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0
http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0
The easiest way to measure distances is using a GUI as VMD software.
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