[gmx-users] Re: implicit wall doesn't recognize the wall_atomtype correctly?

Qiao Baofu qiaobf at gmail.com
Sat Jan 16 23:41:28 CET 2010


Firstly, regarding my last email, even though I didn't get any complain
about the nonsense setting for the wall_atomtype from grompp, the mdrun is
crashed after some steps.

Then I tested some atomtypes which have been given in OPLS, and checked the
output in md.log:
a) When "wall_atomtype = opls_135" in .mdp,
*wall_atomtype[0]=2*(wall_atomtype[1]=2)  in md.log.
b) When "wall_atomtype = SI" in .mdp,  *
wall_atomtype[0]=9*(wall_atomtype[1]=9)  in md.log.
c) When "wall_atomtype = opls_1001" in .mdp,
*wall_atomtype[0]=9*(wall_atomtype[1]=9)  in md.log, where opls_1001
is the atome type for
graphene carbon added by myself.

Does anyone know about why the md.log give different result from the .mdp
file? and what does the *wall_atomtype[0]=2 (or 9)* means?  Thanks a lot in

best wishes,
Baofu Qiao

2010/1/15 Baofu Qiao <qiaobf at gmail.com>

>  Hi all,
> I want to know whether it is a bug or not: When I use some nonsense
> wall_atomtype for the implicit wall, the grompp doesn't complain about it.
> Or it is a mistake I make myself.
> I am using gmx 4.0.7.  See the following flags of wall_atomtype.
> nwall                        = 2
> wall_type                = 9-3
> wall_r_linpot           = 0.1
> wall_atomtype        = *abc   123    ;opls_abc  opls_abc*
> wall_density           = 144 144
> wall_ewald_zfac    = 3
> best wishes,
> Baofu Qiao

Sincerely yours,
Dr. Baofu Qiao
Institute of Computational Physics,
University of Stuttgart
TEL:+49-711-685 63607
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