Thanks David! That helped a lot. I'm now trying to use the walls feature with a user-defined potential. My mdp file is shown below:
title = Alkanethiol SAM MD ; Run parameters integrator = md ; leap-frog integrator nsteps = 500000 ; 2 * 500000 = 1000 ps, 1 ns dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps energygrps = CH3 CH2 S wall0 energygrp_table = CH3 wall0 CH2 wall0 S wall0 ; Bond parameters continuation = yes ; Restarting after NPT 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 cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) coulombtype = Cutoff rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) vdwtype = User rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; 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 = System ; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; Pressure coupling on in NPT ; Periodic boundary conditions pbc = xy ; 3-D PBC ; Dispersion correction DispCorr = no ; account for cut-off vdW scheme ; Walls nwall = 1 wall_type = table wall_atomtype = wall0 ; Velocity generation gen_vel = no ; Velocity generation is off I've defined three energy groups in my system (CH3, CH2, and S), and I have built the following three energy group tables: table_CH3_wall0.xvg table_CH2_wall0.xvg table_S_wall0.xvg I'm not sure whether I should list wall0 among the [ atomtypes ]... When I do, grompp complains about wall0 not being found in the index file. I could add it, but since wall0 doesn't correspond to any actual atoms in my system, I'm not exactly sure how to proceed. In summary, I'm confused as to how to combine the concepts of energy groups and walls when using potential tables. Thank you so much! Olivia On Sat, Nov 26, 2011 at 10:13 AM, David van der Spoel <sp...@xray.bmc.uu.se>wrote: > On 2011-11-26 15:58, Olivia Waring wrote: > >> Hello all, >> >> I'm wondering if it's possible to use tables to simulate a z-dependent >> 12-3 potential. I'd have the following function: >> >> V(z) = C12/(z-z0)^12 - C3/(z-z0)^3 >> >> and I'm trying to construct a table to match. Any hints to get me >> started would be greatly appreciated. >> >> If you mean z as just one cartesian coordinate you should look into the > wall potential options. > > Otherwise you plot the function in tables as a function of z-z0, since it > will be used with the distance. This is in the manual... > > > Thank you! >> Olivia >> >> >> -- >> Olivia Waring >> Princeton University '12 >> AB Chemistry >> >> >> >> > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > --
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