[gmx-users] lincs problems in solvated system

[Manohar Murthi]

hi gmxers

i'm able to run simulations of my molecule in vacuum
for a long period of time (>1ns). the same is true for
simulations of my solvent. however, when i solvate the
molecule using genbox and then attempt an md run
(either npt or nvt) after a successful energy
minimization, i start to get lincs problems within a
few (<20) picoseconds. i've checked that there are no
overlaps or close contacts in the system and tried
several permutations of vdw & coulomb cut-offs,
switched vdw interactions, and pme, but to no avail. 

the lincs errors are typically between solvent atoms
rather than atoms in my main molecule.

any insights would be greatly appreciated.

thanks
mo


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