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

Berk Hess gmx3 at hotmail.com
Fri Jan 15 11:09:53 CET 2010


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.


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

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      =   


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:


Why not use the tabulated wall potential?
That does not require are changes to the code.


    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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