Dear Gromcas Users, I am trying to run membrane protein simulation with slab geometry and EW3DC method (ewald-geometry = 3dc). As mentioned in the article http://www.cell.com/biophysj/abstract/S0006-3495%2803%2974458-0?mobileUi=0 , I have set up my system with extended Z-dimension and used pbc = xyz. While running grompp, I experienced a warning as shown below,
WARNING 1 [file NPT.mdp]: With PME and ewald_geometry = 3dc you should use pbc = xy Is it safe to neglect this warning?, Though, I carried out equilibration with EW3DC method and pbc=xyz, the membrane got distorted. Can anybody help me to figure what is going wrong with my simulation? Below is the mdp file I used for equilibration. define = -DPOSRES_ON integrator = md dt = 0.001 nsteps = 25000 nstlog = 1000 nstxout = 1000 nstvout = 1000 nstfout = 1000 nstcalcenergy = 100 nstenergy = 1000 ; cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 coulombtype = pme rcoulomb = 1.2 vdwtype = Cut-off vdw-modifier = Force-switch rvdw_switch = 1.0 rvdw = 1.2 ; ewald-geometry = 3dc ;slab geometry pbc = xyz ; tcoupl = V-rescale tc_grps = Protein POPC Cal_CL_SOL tau_t = 0.5 0.5 0.5 ref_t = 305.0 305.0 305.0 ; pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 5.0 compressibility = 4.5e-5 0 ;0 for z-direction due to vaccum slab ref_p = 1.0 1.0 ; constraints = h-bonds constraint_algorithm = LINCS continuation = yes ; nstcomm = 100 comm_mode = linear comm_grps = Protein_POPC Cal_CL_SOL ; refcoord_scaling = com Many thanks in advance Anu -- 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.