i want to simulate a system having membrane and proteins with pbc=no to allow surface effects. I use the following settings in my production mdp file :
Run parameters integrator = md ; leap-frog integrator nsteps = 100000000 ; 2 * 100000000 = 2 ms dt = 0.002 ; 2 fs ; Output control ;trr file nstxout = 500000 ; save coordinates every 1ns nstvout = 500000 ; save velocities every 1ns nstenergy = 10000 ; save energies every 20ps nstlog = 10000 ; update log file every 20ps ;xtc file nstxtcout = 10000 ; xtc compressed trajectory output every 20 ps ; Bond parameters constraint_algorithm = LINCS ; holonomic constraints constraints = none ;ns-type = simple nstlist = 0 rlist = 0 coulombtype = Cut-off rcoulomb = 0.0 rvdw = 0 Periodic boundary conditions pbc = no ; 3-D PBC ; Velocity generation gen_vel = YES ; Velocity generation is on comm_mode = ANGULAR however i get LINCS warning and also the log file says this : Your simulation settings would have triggered the efficient all-vs-all kernels in GROMACS 4.5, but these have not been implemented in GROMACS 4.6. Also, we can't use the accelerated SIMD kernels here because of an unfixed bug. The reference C kernels are correct, though, so we are proceeding by disabling all CPU architecture-specific (e.g. SSE2/SSE4/AVX) routines. If performance is important, please use GROMACS 4.5.7 or try cutoff-scheme = Verlet. kindly suggest something .. -- Best *,* Antara -- J.R.F.(Project) Systems Biology Group CSIR - Institute of Genomics & Integrative Biology South Campus, New Delhi-110020 M:+91-9717970040 -- -- 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.