[gmx-users] Using tables to construct a z-dependent 12-3 potential

[David van der Spoel]

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)
> 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.

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 
nonsense though...
If all else fail grep for wall in the source code :).

>
> Thank you so much!
> Olivia
>
>
> 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
>         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
>     <tel:%2B46184714205>.
>     spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>     http://folding.bmc.uu.se
>     --
>     gmx-users mailing list gmx-users at gromacs.org
>     <mailto:gmx-users at 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-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
>     <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