Dear all, I use md-vv and SHAKE algorithm however I face an error which I was not before. Before I had 1-decanol and water system and now I have cis-pionic and water system.
I exactly use the same .mdp file just as before however this error comes : SHAKE is not supported with domain decomposition and constraint that cross charge group boundaries, use LINCS Do you have any idea why I am getting this error which I was not getting before? MDP FILE: integrator = md-vv dt = 0.002 nsteps = 8000000 ; 16 ns ; Output control nstxout = 2000 nstvout = 2000 nstlog = 2000 nstenergy = 2000 ; Bond parameters continuation = no ; Initial simulation constraint_algorithm = shake ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained shake_tol = 0.0001 ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling ; tcoupl is implicitly handled by the sd integrator tcoupl = nose-hoover tc-grps = System tau_t = 1.0 ref_t = 300 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; Velocity generation is on gen_temp = 300 ; temperature for velocity generation gen_seed = -1 ; random seed ; COM motion removal ; These options remove COM motion of the system nstcomm = 10 comm-mode = Linear comm-grps = System thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.