[gmx-users] Fwd: Problem in applying walls in the z direction

[Stephen Chan]

I started from the original pdb file without any wrapping. I changed the 
mdp for the wall settings to:

pbc                     = xy
nwall                   = 2
wall-type               = 9-3
wall-density            = 5  5
wall-atomtype           = OT OT
wall-r-linpot           = 0.1
ewald-geometry          = 3dc

When running the minimization, I got the following error:

Steepest Descents:
    Tolerance (Fmax)   =  1.00000e+03
    Number of steps    =        50000
            Step           Time         Lambda
               0        0.00000        0.00000

    Energies (kJ/mol)
            Bond            U-B    Proper Dih.  Improper Dih. CMAP Dih.
     6.25781e+03    4.25192e+04    3.95501e+04    5.25750e+02 -9.41068e+01
           LJ-14     Coulomb-14        LJ (SR)   Coulomb (SR) Coul. recip.
     9.76917e+03   -1.30464e+03           -nan           -nan 2.66520e+04
  Position Rest.     Dih. Rest.      Potential Pressure (bar) Constr. rmsd
     7.48006e-01    1.57819e+03           -nan           -nan 2.39158e-06

I wonder if there are atoms located too closely to the walls or if the 
parameters for the wall settings are wrong.

Stephen


On 07/02/16 22:27, Stephen Chan wrote:
> I notice that they are the hydrogen atoms of the same water molecule 
> and they may have been split by the PBC in the previous step. I'll 
> prepare the gro again. Thanks for your help.
>
> Cheers
>
> On 07/02/16 22:23, Justin Lemkul wrote:
>>
>>
>> On 7/2/16 4:20 PM, Stephen Chan wrote:
>>> Hi Justin,
>>>
>>> Just above the fatal error message, there is some additional 
>>> information:
>>>
>>> Initializing Domain Decomposition on 112 ranks
>>> Dynamic load balancing: auto
>>> Will sort the charge groups at every domain (re)decomposition
>>> Initial maximum inter charge-group distances:
>>>     two-body bonded interactions: 10.867 nm, Exclusion, atoms 30544 
>>> 30545
>>>   multi-body bonded interactions: 0.488 nm, CMAP Dih., atoms 1075 1091
>>> Minimum cell size due to bonded interactions: 11.954 nm
>>> Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 
>>> 0.222 nm
>>> Estimated maximum distance required for P-LINCS: 0.222 nm
>>> Guess for relative PME load: 0.23
>>> Will use 84 particle-particle and 28 PME only ranks
>>> This is a guess, check the performance at the end of the log file
>>> Using 28 separate PME ranks, as guessed by mdrun
>>> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
>>> Optimizing the DD grid for 84 cells with a minimum initial size of 
>>> 14.942 nm
>>> The maximum allowed number of cells is: X 0 Y 0 Z 2
>>>
>>> Do I need to adjust other parameters in the mdp accordingly??
>>>
>>
>> No, you need to investigate this:
>>
>>   two-body bonded interactions: 10.867 nm, Exclusion, atoms 30544 30545
>>
>> Bonded interactions are normally within 1.5 nm or so.  A distance 
>> this large suggests something bizarre going on in your topology. 
>> Figure out what these atoms are and what is going on with them.
>>
>> -Justin
>>
>