Hi, I am running a pulling simulation with implicit solvent using Gromacs 4.5.5, single precision on 8 CPU, with OPLS-AA FFT.
The system is equilibrated for 10 ns, with pbc=0 and infinite cut-off (.mdp file is posted). I do not get any LINC errors for the equilibration, however when I start pulling the protein with infinite cut-off, after 10-15 nm extension (this is about 1500 ps with pulling rate=0.01 nm/ps), the system crashes due to the LINC errors. For different runs, the LINC errors are for different atoms. I have tried pulling rates =0, 0.001, 0.01, and 0.1 nm/ps, but even for pulling rate=0, I always get the LINC errors with infinite cut-off in implicit solvent. When I use a finite cut-off distance (4, 6, 8, 10, and 20 nm), there is no LINC error and I can unfold the protein to the full extension. If I run the simulation with cut-off of 40 nm, I get the same errors as infinite cut-off. The size of the folded protein is less than 4 nm, the unfolded protein is about 35 nm. I ran a one step simulation for a folded protein, and the GB and energy terms are the same for cut-off distances of 6,8,10,20,30,40 and Infinit. There is no LINC error in vacuum dielectric=80 with infinite cut-off. My question is if there is something wrong in my .mdp file? or this is an issue with GB calculation? Is there any way to avoid LINC errors in the pulling simulation with implicit solvent and infinite cut-off? For version Gromacs 5.0.4, I have some issues with running the simulations in parallel, so version 4.5.5 is the only available option. Thank You, Mona ; Run parameters integrator = sd ld_seed =-1 dt = 0.001 tinit = 0 nsteps = 5000000 nstcomm = 10 ; Output parameters nstxout = 1000 nstvout = 1000 nstfout = 1000 nstxtcout = 1000 nstenergy = 1000 ; Bond parameters constraint_algorithm = lincs constraints = h-bonds ; H bonds constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy continuation = yes ; continuing from NVT comm_mode = ANGULAR cutoff_scheme = group pbc = no ; Periodic boundary conditions disabled coulombtype = cut-off ; Calculate coulomb interactions using cutoff rcoulomb = 0.0 ; Coulomb cutoff of infinity vdw_type = cut-off ; Calculate van der Waals interactions using cutoff rvdw = 0.0 ; Van der Waals cutoff of infinity rlist = 0.0 ; Neighbor list cutoff nstlist = 0.0 ; Do not update neighbor list tau_t = 2 ref_t = 300 implicit_solvent = GBSA gb_epsilon_solvent = 80 gb_saltconc = 0.10 gb_algorithm = OBC rgbradii = 0.0 sa_surface_tension = 2.25936 ; Pull code pull = umbrella pull_geometry = distance ; simple distance increase pull_dim = N N Y pull_start = yes ; define initial COM distance > 0 pull_ngroups = 1 pull_group0 = Freeze pull_group1 = Pull pull_rate1 = 0.001 ; nm per ps pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout = 1000 pull_nstfout = 1000 -- 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.