Dear Gromacs users, I have a question about an effect of time-step on results of simulation with LINCS.
Now, I am running on a MD simulation of a rigid molecule in vacuum under NVE ensemble. No temperature coupling was used. No inter-atomic potential was used. The rigid molecule is consisting of just three atoms and the geometry of the molecule is triangle. We are using LINCS to constrain all bond length. We have run simulations with different time steps. The initial velocities of each atom was defined in .gro and the initial velocities were identical at different times steps. In calculation results, the bond lengths were successfully constrained at each time step. However, when the smaller time step, the kinetic energy of the rigid molecule increased with an increase in simulation time. (At other time steps, the kinetic energies were almost constant.) I cannot understand why the kinetic energy was increased at "smaller" time step. Is this derived from LINCS algorithm, or not? Please give me a suggestion. Thanks in advance for your help. Hideya Nakamura ------------------------------------------------------------------------------------------------ The .mdp file and .top file were shown as follows: ------------------------------------------------------------------------------------------------ ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit = 0 dt = 0.00002 ;[ps] nsteps = 250000000 ;[STEP] ; ;nsteps = 1000 ;[STEP] ; number of steps for center of mass motion removal = ;nstcomm = 1 ;(1) ; mode for center of mass motion removal comm-mode = None ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ;[step] ; ns algorithm (simple or grid) = ns_type = grid ; nblist cut-off = [nm] rlist = 1.5 ; Periodic boundary conditions: xyz or none = pbc = xyz ;OPTIONS FOR TEMPERATURE COUPLING tcoupl = no tc_grps = TRI tau_t = 0 ;[ps] ref_t = 350 ;[K] ;OPTIONS FOR PRESSURE COUPLING Pcoupl = no ;Pcoupl = Parrinello-Rahman Pcoupltype = isotropic ;useful for membrane tau_p = 1.5 ;[ps] compressibility = 4.5e-05 ;[bar^-1] ref_p = 1.01325 ;[bar] ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = no ;yes or no gen_temp = 323 ;[K] gen_seed = 173529 ;(173529) ; OPTIONS FOR BONDS = constraints = none ;all-bonds/none ; Type of constraint algorithm = constraint-algorithm = LINCS ; Do not constrain the start configuration = unconstrained-start = no ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 4 ;(4) ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 ;(30) ------------------------------------------------------------------------------------------------------------------------ [ system ] ; name 1 triangle in Vacuum [ moleculetype ] ; name nrexcl TRI 1 [ defaults ] 1 1 yes 0.5 0.5 [ atomtypes ] ;name at.num mass charge ptype c6 c12 AA 79 196.96655 0.000 A 0.00000E+00 0.00000E+00 [ atoms ] ; nr type resnr residu atom cgnr charge 1 AA 1 TRI 1AA 1 0.000 2 AA 1 TRI 2AA 2 0.000 3 AA 1 TRI 3AA 3 0.000 [ constraints ] ; ai aj funct b0 1 2 1 0.408 1 3 1 0.408 2 3 1 0.408 [ exclusions ] 1 2 3 2 1 3 3 1 2 [ molecules ] ; name number TRI 1 ------------------------------------------------------------------------------------------------------------------------ -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists