[gmx-users] 10-4-3 implicit wall potential

[Baofu Qiao]

Hi,

Thanks a lot!
I just tried again. "mdrun -table table" works.

best regards,
Baofu Qiao

Berk Hess wrote:
> Hi,
>
> Do you really need all those tables?
> I would think you onkly need to specify your wall table and no other tables.
>
> As the documentation says (I think), the cut-off for the wall table is the length
> of the table you specify.
>
> Berk
>
> Date: Fri, 15 Jan 2010 11:02:40 +0100
> From: qiaobf at gmail.com
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] 10-4-3 implicit wall potential
>
>
>
>
>
>
>   
>   
>
>
> Dear prof. Berk,
>
>
>
> Since it is the first time I use the tabulated potential, I have lots
> of questions about it. Could you help me out? Thanks a lot!
>
>
>
> I make the test in the system with only some waters between 2 implicit
> walls.
>
> 1. some related parameters of the .mdp file are listed  below. Is there
> anything wrong? 
>
> energygrps               = SOL
>
> pbc                            = xy
>
> rlist                            = 1.2
>
> coulombtype           = pme
>
> rcoulomb                 = 1.2
>
> vdw-type                 = cut-off
>
> rvdw                         = 1.2
>
> DispCorr                  = EnerPres
>
> table-extension       = 1
>
> energygrp_table      =   
>
> ;Walls
>
> nwall                         = 2
>
> wall_type                  = table 
>
> wall_r_linpot             = 0.0
>
> wall_atomtype          = opls_135 opls_135   
>
> wall_density              =     ;(the wall_density is included in
> the tabulated potential, right?)                
>
> wall_ewald_zfac      = 3
>
>
>
> 2.  The flags of mdrun are:
>
>       mdrun -deffnm table  -tablep table_SOL_wall0.xvg
> table_SOL_wall1.xvg -table table.xvg
>
> where table.xvg is copied from  gmx_top_path/table6-12.xvg, and
> table_SOL_wall0.xvg and table_SOL_wall1.xvg are the self-generated 9-3
> potential (9-3 potential is used for the aim of testing and compare
> with the  default 9-3 potential of gromacs.)
>
> Since I use only the tabulated potential between SOL-wall0 and
> SOL-wall1, why do I need the table.xvg?  Does it affect the coulomb/vdw
> potential between SOL-SOL?
>
>
>
> 3. In the table_SOL_wall0.xvg and table_SOL_wall1.xvg, the distance
> range of 0-3nm is generated. max(rvdw, rcoulomb)=1.2 nm and
> table-extension=1. The question is what is the cutoff distance for
> the tabulated SOL-wall0/wall1 potential, 2.2nm or 3nm?
>
>
>
> 4. In the output file table.log,
>
> Table routines are used for coulomb: TRUE
>
> Table routines are used for vdw:     FALSE
>
> Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
>
> Cut-off's:   NS: 1.2   Coulomb: 1.2   LJ: 1.2
>
> System total charge: 0.000
>
> Generated table with 1100 data points for Ewald.
>
> Tabscale = 500 points/nm
>
> Generated table with 1100 data points for LJ6.
>
> Tabscale = 500 points/nm
>
> Generated table with 1100 data points for LJ12.
>
> Tabscale = 500 points/nm
>
> Reading user tables for 1 energy groups with 2 walls
>
> Read user tables from table_SOL_wall0.xvg with 1501 data points.
>
> Tabscale = 500 points/nm
>
> Read user tables from table_SOL_wall1.xvg with 1501 data points.
>
> Tabscale = 500 points/nm
>
>
>
> The question are: 
>
> a) Since Table is not used for vdw (FALSE),  why table is generated
> for LJ6/LJ12?
>
> b) Where does the value of  "1100" data points come from? (Since
> rvdw=1.2, tabscale=500, it should be 1400, not 1100!?)
>
> c) 1501 data points is generated for table_SOL_wall0/wall1, the answer
> of the 3rd question (cutoff value for the tabulated potential
> calculation) should be 3nm, right?
>
>
>
> Sorry for the lots of questions!
>
>
>
> best wishes,
>
> Baofu Qiao
>
>
>
> Berk Hess wrote:
>
>   Hi,
>
> Why not use the tabulated wall potential?
> That does not require are changes to the code.
>
> Berk
>
>   
>   
>     Date: Tue, 5 Jan 2010 14:13:30 +0100
> From: qiaobf at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] 10-4-3 implicit wall potential
>
> HI all,
>
> Does anyone have experience to implement the 10-4-3 implicit wall
> potential?  If I want to use it, which files do I need to change, except
> wall.c? Can anyone give some suggestions?
>
> Thanks a lot!
>
> best wishes,
> Baofu Qiao
>