[gmx-users] 10-4-3 implicit wall potential
Baofu Qiao
qiaobf at gmail.com
Fri Jan 15 11:52:27 CET 2010
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
>
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