Constraints defined for a bond not working during simulation.
If you defined constraints (constraints difined in .itp file) for a perticular bond and run the simulation with this constraints.After the simulatons gets over I have noticed that bond distance didn't remain constant and it oscillate with 0.3 to 0.5 nm.
Example. If I put the constraints for AB bond should be 0.35 nm. After ploting g_dist I noticed it oscillate bewteen 1.1 nm to 5 nm. Expected is AB should remain constant 0.35 nm through out the simulation.
#4 Updated by Berk Hess about 9 years ago
Please answer on the bugzilla.gromacs.org page,
there is a link in the mail that you can click.
You already attached solute.itp before.
The problem is that nor the top file, neither one of the itp
files included in there includes solute.itp.
You can define a constraint in solute.itp, but if the file
is not used, the constraint is not used.
#5 Updated by Berk Hess about 9 years ago
This is almost certainly not a bug in Gromacs,
but an error in your files, or more likely due to a mistake
in your procedure to set up the simulation.
I don't have the time to look into the problems of users.
Please check your input, several options:
If necessary, read the documentation,
double check the topology setup,
use grompp -pp and check the processed output for the [ constraint ]
(and make the the moleculetype matches the one in your [ system ].
run gmxcheck -s1 ... -s2 ... on the tpr with and without constraint
to see what the differences are.
Only when you have triple checked everything and still have problems,
first search the gmx-users list and then post there if you did
not find a solution.