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.abra...@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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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