[gmx-users] lincs problems

Mark Abraham mark.abraham at anu.edu.au
Wed Dec 5 01:22:02 CET 2007

> Dear all,
> I am trying to simulate a ligand at the cavity of CB receptor with the
> dmso environment. Even if I used very large number of steps for the
> geometry optimization before simulation, I have some LINCS problem for the
> solvent, I changed the solvent from dmso to water, but it didn't help the
> solution.

http://wiki.gromacs.org/index.php/Errors#LINCS_warnings tells you a bit
about this situation. There's some useful advice on alternatives for
system preparation here
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation. In
particular, you may wish to see if you can do EM and simulate in vacuo.
Also starting your first MD run with position restraints is normally a
good plan.

> The input and output files are in below.

They look OK to me.


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