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

[Olivia Waring]

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
<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.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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