[gmx-users] LINCS constraint on DU-DU bond

[Alessandra Villa]

Hi,

On Fri, Dec 13, 2019 at 1:53 PM Luirink, R.A. <r.a.luirink at vu.nl> wrote:

> Hi,
> I would like to constrain a bond between two dummy atoms using LINCS
> constraints. As I want to perturb the atoms towards a N-H bond, I would
> like to pre-treat it as such, due to the low mass of one of the dummy atoms.
> Is this possible somehow? And, if not, how is the constraint introduced
> during the perturbation from DU to H atom?
> (using gromacs version 2018.6)
>

As far as I understood you want to go from state A (DU-DU) to state B
(N-H), probably to calculate some free energy difference,
you could add manually the constrain the two atoms in your topology file
using the [ constraints ] ( for the syntax look at
http://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html?highlight=topology
).
You can use gmx dump -s to check your tpr file

Best regards

Alessandra



> Thanks in advance,
> Rosa
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