[gmx-users] domain decomposition

mohsen ramezanpour ramezanpour.mohsen at gmail.com
Tue Apr 5 09:09:59 CEST 2011

Dear Mark

Actually I don't know why.
I just did the normal process as other my simulations.

Let me discribe my work in details:
I had a protein and a drug,I separated all residues around my drug (2 nm in
radius) by PYMOL
Then I saved the result as protein-new.pdb
So.I used pdb2gmx to generate .top and .gro file for this .pdb file
I entered the following commands for pdb2gmx:
pdb2gmx  -f  protein-new.pdb  -o  protein-new.gro   -p   topology.top
-water  spc  -ignh
and I used Gromos 43a1 force field.

when I want to do EM there are an additional error that  results in crashing
the mdrun:
Warning: 1-4 interaction ...  your system is exploding

it says modifying interaction tables!

Besides,I checked my pdb file,atoms 922 and 943 and 2 others who have bad
interactions,all of them are N atom of residues!

Thanks in advance for your reply

On Sun, Apr 3, 2011 at 8:33 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> On 4/04/2011 1:51 AM, mohsen ramezanpour wrote:
>> Dear All
>> I have a file which contains afew residues (noncontinuous),
>> When I use mdrun on a computer(4 cpu) I am facing with the following
>> Error:
>> Fatal error:
>> There is no domain decomposition for 4 nodes that is compatible with the
>> given box and a minimum cell size of 3.28697 nm
>> Change the number of nodes or mdrun option -rdd
>> Look in the log file for details on the domain decomposition
>> it is relating to domain decomposition,
>> Besides I checked either restraining residues and not restraining.But it
>> dosn't differed
>> I changed the number of nodes to 1 but it didn't work!
>> mpirun   -np  1  mdrun   -v   -deffnm  EM
>> Besides I looked in the log file and the important part of it was:
>> Initializing Domain Decomposition on 4 nodes
>> Dynamic load balancing: no
>> Will sort the charge groups at every domain (re)decomposition
>> Initial maximum inter charge-group distances:
>>    two-body bonded interactions: 2.988 nm, LJ-14, atoms 922 943
>>  multi-body bonded interactions: 2.988 nm, Proper Dih., atoms 922 943
>> Minimum cell size due to bonded interactions: 3.287 nm
>> Using 0 separate PME nodes
>> Optimizing the DD grid for 4 cells with a minimum initial size of 3.287 nm
>> The maximum allowed number of cells is: X 1 Y 1 Z 1
>> please let me know how can I solve this problem.
>> Thanks in advance
> Why do you have bonds nearly 3nm long?
> Mark
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