[gmx-users] Using tables to construct a z-dependent 12-3 potential
David van der Spoel
spoel at xray.bmc.uu.se
Sat Nov 26 22:08:29 CET 2011
On 2011-11-26 21:01, Olivia Waring wrote:
> 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)
> 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:
> 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.
I think you have to select a wall_atomtype that is a true atomtype in
your force field, since it uses this for the force field parameter.
Please check the manual again, I've never used this feature myself, but
I would guess that all atoms interact with the wall through the table
where a combination rule is used to get the parameters. This could be
If all else fail grep for wall in the source code :).
> Thank you so much!
> On Sat, Nov 26, 2011 at 10:13 AM, David van der Spoel
> <spoel at xray.bmc.uu.se <mailto:spoel at 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
> 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 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
> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> 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-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
More information about the gromacs.org_gmx-users