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
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