Dear users, I am trying to run a coarse grained simulation of a membrane protein in a mixed lipid billayer using martini model 2.2. I have already performed all the equilibration steps successfully on my desktop with GROMACS 5.1.0. However, when i try to execute its production run in parallel(having gromacs 5.1 version installed) it complains of LINCS warning and terminates at step 0. The lincs warning error is coming from BB and SC1 atoms of one of the protein residues.
But on the contrary, it runs on the desktop successfully. *My production run mdp file details are below :* . This is the MD.mdp file :ntegrator = md tinit = 0.0 dt = 0.020 nsteps = 2500000000 nstxout = 2000 nstvout = 2000 nstfout = 2000 nstlog = 2000 nstenergy = 2000 nstxtcout = 2000 xtc_precision = 100 ns_type = grid pbc = xyz nstlist = 10 cutoff-scheme = Verlet rlist = 1.2 vdwtype = Cut-off vdw-modifier = none rvdw_switch = 1.0 rvdw = 1.2 coulombtype = pme rcoulomb = 1.2 tcoupl = v-rescale tc-grps = protein CHOL_POPC_DPSM_DPCE W_ION tau_t = 1.0 1.0 1.0 ref_t = 303.15 303.15 303.15 ; Pressure coupling: Pcoupl = berendsen Pcoupltype = semiisotropic tau_p = 5.0 5.0 compressibility = 3e-4 3e-4 ref_p = 1.0 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN: gen_vel = no refcoord_scaling = all *the command used for mdrun :* -deffnm MD -pin on -rdd 1.8 -np 16 I would also like to mention that i generated the initial structure of the system using CHARMM GUI MARTINI MAKER protein-membrane system option. I have followed the exact builder protocol for the equilibration and minimisation. Kindly suggest something! Thanks, Antara -- Junior research fellow(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 [email protected].
