[gmx-users] Wall potential for a membrane simulation
Hello, I would like to simulate a membrane system with two walls, one at the bottom of my box at z=0 and one at the top, using the gromos53a6 forcefield (GROMACS version 4.5.5). My testing system consists of a membrane in the middle, water and sodium ions (40xNa+) above the membrane and water and chloride ions (40 Cl-) beneath it. First, I built up the system, did an energy minimization and then implemented the walls for the npt-equilibration. I didn't change anything in the topology. (Do I have to define the wall-atom-type there?If yes, what exactly do I have to put in the topology?) The interesting part of my nvt.mdp file looks like that: nwall = 2 wall_type = 10-4 wall_density = 100 100 wall_atomtype = C C wall_r_linpot = 1 1 ; with -1 I got a fatal error, because atoms were beyond the wall wall_ewald_zfac = 3 ewald_geometry= 3dc pbc = xy; Periodic Boundary Conditions in x/y direction What I see in VMD is the following: as expected some NA-ions are going through the membrane to reach the chloride/water side. But at the same time water molecules (and one chloride-ion) at both sides disappear in z-direction and never come back. In the first 10ps (with a tiny time step of 0.1fs) there were only a few molecules that went outside the box, but after 10 ps it increased dramatically and at some point the equilibration crashed. I already played around with time-steps, atom-types and the density, but couldn't find anything that works to keep the molecules inside the box... Anyone has an idea what I did wrong and how I can correct it? Unfortunately there is not much about that in the manual and I could not find anything that really helped me in the mailing-list archive Thanks in advance!!! Cheers, Marianne Schulte -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Wall potential for a membrane-simulation
Hi everyone! I'm new to Gromacs and trying to simulate a membrane system with two walls, one at the bottom of my box at z=0 and one at the top, using the gromos53a6 forcefield (GROMACS version 4.5.5). My testing system consists of a membrane in the middle, water and sodium ions (40) above the membrane and water and chloride ions (also 40) beneath it. First, I built up the system, did an energy minimization and then implemented the walls for the nvt-equilibration. I didn't change anything in the topology. (Do I have to define the wall-atem-type there? If yes, what exactly do I have to put in the topology?) My nvt.mdp file looks like that: title = NVT equilibration for KALP15-DPPC define = -DSTRONG_POSRES -DPOSRES_LIPID ; position restrain the lipid ; Run parameters integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= yes ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; 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 is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = lipid SOL_NA_CL ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 303 303 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions ;wall nwall = 2 wall_type = 10-4 wall_density = 100 100 wall_atomtype = C C wall_r_linpot = 1 1 ; with -1 I got a fatal error, because atoms were beyond the wall wall_ewald_zfac = 3 ewald_geometry= 3dc pbc = xy ; Periodic Boundary Conditions in x/y direction ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 303 ; temperature for Maxwell distribution gen_seed= -1 ; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions ns
[gmx-users] Wall potential
Hi Gomacians, I want to use implicit wall. I set the mdp parameters as follows. nwall= 2 wall_type= 9-3 wall_r_linpot= 1 wall_atomtype= Au Au wall_density = 58.01 58.01 wall_ewald_zfac = 3 Also set LJ parameters in topology file. Au196.9665 0.000 A 6.53000e-02 3.40800e-01 ; Gold However, In mdout file i get nwall= 2 wall_type= 9-3 wall_atomtype[0] = 7#why 7? wall_atomtype[1] = 7 wall_density[0] = 58.01 wall_density[1] = 58.01 wall_ewald_zfac = 3 System-wall00.0e+00 -1.17533e+020.0e+000.0e+00 System-wall10.0e+00 -2.41204e-010.0e+000.0e+00 wall0-wall00.0e+000.0e+000.0e+000.0e+00 wall0-wall10.0e+000.0e+000.0e+000.0e+00 wall1-wall10.0e+000.0e+000.0e+000.0e+00 Is this an error? can somebody tell me how 9-3 wall parameters are calculated in gromacs? Do I need to specify anything else? Thanks in advance -- Abhijeet -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Wall Potential
Hi all, I am trying to simulate multiple (2 or 3) tetrapeptides in a cage with Gromacs. However, I would like to constrain the peptides to the centre of the box by enforcing a wall potential in which each of the atoms of the peptide feels a repulsive potential with respect to the edge of the box (or a spherical cage). I am wondering is Gromacs able to perform simulations with such conditions? Any other alternative suggestions with similar functions are greatly appreciated. Many thanks. -- Best regards, Huey Ling ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
