[gmx-users] Too many LINCS warnings with CaDA model, User-defined potential, Stochastic dynamics integrator

[Srinath Kompella]

Dear All,
              Using GROMACS-5.1.4, I am trying to reproduce the results of
a metal-ligand coordination-directed self-assembly study. The metal ion
Pd(II) is represented using a CaDA model where four identical dummy atoms
each with charge +0.5 are coplanarly attached to the Pd with charge 0.0. A
united-atom approach is applied for modeling the organic neutral ligand.
Since the system is not charge neutral, generalized reaction field method
is used for electrostatics. To take the solvent effects (treated implicitly
as a continuum medium) into account, SD integrator, different near- and
far-field dielectric constant values are set, and WCA potential is applied
for ligand-ligand interactions. All bonds are constrained using LINCS, and
the timestep is 5 fs.

              The authors of the original work had modified the source code
to employ WCA interaction. I am using GROMACS user-defined potential tables
for all the vdW interactions, i.e., WCA between the ligand atoms and LJ for
the rest. I have modified their topology file and made a .mdp file
accordingly (attached here).

              After energy minimizing the system, NVT equilibration crashes
with the error "too many LINCS warnings". From the log file, and through
visual inspection, I noticed that the bonds and angles of the cations
(Pd(II) CaDA model) change in a bizarre fashion and cause the error. I've
experimented with smaller timesteps and slow ramping of temperature, but
only for timestep of 3 fs or smaller, the simulations run without any LINCS
error. Since a timestep of 5 fs was used in the original work, and I would
like to use the same, kindly help me understand where I am doing wrong and
correct it.

              Thank you in advance.

-- 
Srinath Kompella
Ph.D. Research Scholar
Molecular Simulations Laboratory,
Chemistry and Physics of Materials Unit (CPMU),
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR),
Jakkur - 560 064, Bangalore,
Karnataka State, India.