[gmx-users] lincs problems in solvated system

Manohar Murthi sir_donald_bradman at yahoo.com
Tue Jul 18 16:42:04 CEST 2006

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.


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