all-bonds option not constraining all bonds?
constraints = all-bonds
in the run .mdp file results in all bond lengths being constrained to the equilibrium value defined by the force field. Does this require some extra magic in the .top file?
My OPLS-AA alcohol simulations with "constraints = all-bonds" have resulted in largely the same results as for "constraints = h-bonds". Now having had a look at the bond length distributions it seems that the H bond lengths are correctly constrained, but the C-C bond lengths are not.
I've used Gromacs 4.0.3 for the simulations.
#2 Updated by Jussi Lehtola over 10 years ago
This is a bit odd.
When I look at the C-C bond in ethanol with an index file I see that it is constrained with all-bonds (normal distribution with std 0.000410457, compared to 0.00326475 with 'none' and 0.00330772 with 'h-bonds').
However the distribution in bonds.xvg given by g_bond is identical for 'h-bonds' and 'all-bonds': there are sharp peaks at 0.95 Å and 1.1 Å and a bell curve at roughly 1.77Å with a standard deviation of 0.6 Å.
#5 Updated by Jussi Lehtola over 10 years ago
(In reply to comment #4)
Can it be that you have a mistake in your index file forr g_bond?
A distance of 0.177 nm is far too long for a C-C bond.
I suspect you are looking at an H-C distance.
Yes, that is what I would think too.
It just came to me that g_hbond has a mandatory index file input. In the run folder I had the file index.ndx that contained the default groups System and EtOH. When run on either of these groups g_hbond produces the distances of all sorts of combinations of pairs.
It would be nice if g_bond gave some warning (or an error, even) about nonexisting bonds if the atoms don't have a bond in the topology..
Thanks for your help, and sorry for the trouble!