[gmx-users] genconf and bonded interactions

[Fabio Affinito]

Thanks.
This actually solved the problem in grompp.
I still have problems when running. This is the log of mdrun:
> Initializing Domain Decomposition on 4096 nodes
> Dynamic load balancing: auto
> Will sort the charge groups at every domain (re)decomposition
> Initial maximum inter charge-group distances:
>     two-body bonded interactions: 0.583 nm, LJ-14, atoms 28051 28056
>   multi-body bonded interactions: 0.583 nm, Proper Dih., atoms 28051 28056
> Minimum cell size due to bonded interactions: 0.642 nm
> Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 1.139 nm
> Estimated maximum distance required for P-LINCS: 1.139 nm
> This distance will limit the DD cell size, you can override this with -rcon
> Guess for relative PME load: 0.43
> Will use 2400 particle-particle and 1696 PME only nodes
> This is a guess, check the performance at the end of the log file
> Using 1696 separate PME nodes
> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
> Optimizing the DD grid for 2400 cells with a minimum initial size of 1.424 nm
> The maximum allowed number of cells is: X 18 Y 18 Z 6
>
> -------------------------------------------------------
> Program mdrun_mpi_bg, VERSION 4.5.4
> Source code file: domdec.c, line: 6438
>
> Fatal error:
> There is no domain decomposition for 2400 nodes that is compatible with the given box and a minimum cell size of 1.4242 nm
> Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings
> Look in the log file for details on the domain decomposition
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> "Meet Me At the Coffee Shop" (Red Hot Chili Peppers)

I imagine that now I have to tune the dds and rcon parameter. Am I right?

Fabio

On 07/27/2011 04:48 PM, Justin A. Lemkul wrote:
>
>
> Fabio Affinito wrote:
>
> This is the key part:
>
>>> processing coordinates...
>>> Warning: atom name 18113 in topol.top and out.gro does not match (MN1
>>> - CN1)
>>> Warning: atom name 18114 in topol.top and out.gro does not match (MN2
>>> - CN2)
>>> Warning: atom name 18115 in topol.top and out.gro does not match (N -
>>> CN3)
>>> Warning: atom name 18116 in topol.top and out.gro does not match (H1
>>> - N)
>>> Warning: atom name 18117 in topol.top and out.gro does not match (H2
>>> - CA)
>>> Warning: atom name 18118 in topol.top and out.gro does not match (H3
>>> - CB)
>>> Warning: atom name 18119 in topol.top and out.gro does not match (CA
>>> - OA)
>>> Warning: atom name 18120 in topol.top and out.gro does not match (HA
>>> - P)
>>> Warning: atom name 18121 in topol.top and out.gro does not match
>>> (MCB1 - OB)
>>> Warning: atom name 18122 in topol.top and out.gro does not match
>>> (MCB2 - OC)
>>> Warning: atom name 18123 in topol.top and out.gro does not match (CB
>>> - OD)
>>> Warning: atom name 18124 in topol.top and out.gro does not match (HB1
>>> - CC)
>>> Warning: atom name 18125 in topol.top and out.gro does not match (HB2
>>> - CD)
>>> Warning: atom name 18126 in topol.top and out.gro does not match (HB3
>>> - OE)
>>> Warning: atom name 18127 in topol.top and out.gro does not match (C -
>>> C1A)
>>> Warning: atom name 18128 in topol.top and out.gro does not match (O -
>>> O1A)
>>> Warning: atom name 18129 in topol.top and out.gro does not match (N -
>>> C1B)
>>> Warning: atom name 18130 in topol.top and out.gro does not match (H -
>>> C1C)
>>> Warning: atom name 18131 in topol.top and out.gro does not match (CA
>>> - C1D)
>>> Warning: atom name 18132 in topol.top and out.gro does not match (HA
>>> - C1E)
>>> (more than 20 non-matching atom names)
>>>
>>> WARNING 1 [file topol.top, line 50]:
>>> 219116 non-matching atom names
>>> atom names from topol.top will be used
>>> atom names from out.gro will be ignored
>>>
>
> This is the root of the problem. Your topology does not match your
> coordinates in terms of the order of the molecules. grompp (and, in then
> later, mdrun) thinks that protein is lipid, lipids are water, etc, so
> you're effectively telling it that things are bonded within a molecule
> when they're not. Even if the simulation initially ran it would blow up
> immediately because you're mapping the wrong coordinates onto the wrong
> molecules.
>
> The coordinate file from genconf is an exact replica of your system, but
> the molecules are not re-ordered in any convenient way. So, for your
> system, instead of:
>
> [ molecules ]
> Protein_A 4N
> Protein_B 4N
> Protein_C 4N
> Protein_D 4N
> POPC 4N
> POPG 4N
> SOL 4N
> K+ 4N
>
> you need this in your topology:
>
> [ molecules ]
> Protein_A N
> Protein_B N
> Protein_C N
> Protein_D N
> POPC N
> POPG N
> SOL N
> K+ N
> (repeated three more times)
>
> Otherwise, reorganize the .gro file. Topology manipulation is probably
> easier, though.
>
> -Justin
>


-- 
Fabio Affinito, PhD
SuperComputing Applications and Innovation Department
CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY
Tel: +39 051 6171794  Fax: +39 051 6132198