[gmx-users] Problem with Group and Verlet cut -off scheme

[Ben Tam]

Hi Justin,


This is what I got from the log file:


Initializing Domain Decomposition on 6 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: 4.882 nm, Bond, atoms 456 457
  multi-body bonded interactions: 4.915 nm, Angle, atoms 457 459
Minimum cell size due to bonded interactions: 5.407 nm
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 6 cells with a minimum initial size of 6.758 nm
The maximum allowed number of cells is: X 0 Y 0 Z 0



But when I check, this the atoms that is limiting (from .gro file) :


    1MOL     C1  455   0.728   1.339   1.541
    1MOL     C2  456   0.696   1.224   1.636
    1MOL     C3  457   0.737   1.220   1.769
    1MOL     C4  458   0.692   1.112   1.851
    1MOL     H4  459   0.713   1.112   1.951


And non of them tells me they are over 4nm, which I am not sure where else it could go wrong. The smallest length of my box is 2 nm and my cut-off length is 1 nm. Thank you for your help.


By the way, do I reply to the gmx-user at gromacs.org address or how do I reply without disturbing other users?


Thank you again,


Ben


________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: 08 July 2016 15:22
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Problem with Group and Verlet cut -off scheme



On 7/8/16 10:20 AM, Ben Tam wrote:
> Hi Mark,
>
>
> It shouldn't, what I am simulated is a crystal structure and my tabulated forcefield is only up to 3nm. Do you think the problem is there? To avoid the charge group, I am putting in the section of [atoms]:
>
>
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
> 1 Mg 1 MOL Mg 1
> 2 O1 1 MOL O1 2
> 3 O2 1 MOL O2 3
> 4 O3 1 MOL O3 4
> .        .      .         .             .       .
>
> .        .      .         .             .       .
>
> .        .      .         .             .       .
>
>
> ... etc.
>
>

The DD setup section of the .log file will tell you exactly what the limiting
interactions are.

-Justin

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