Dear Mark<br><br>Actually I don't know why.<br>I just did the normal process as other my simulations.<br><br>Let me discribe my work in details:<br>I had a protein and a drug,I separated all residues around my drug (2 nm in radius) by PYMOL<br>
Then I saved the result as protein-new.pdb<br>So.I used pdb2gmx to generate .top and .gro file for this .pdb file<br>I entered the following commands for pdb2gmx:<br>pdb2gmx -f protein-new.pdb -o protein-new.gro -p topology.top -water spc -ignh <br>
and I used Gromos 43a1 force field.<br><br>when I want to do EM there are an additional error that results in crashing the mdrun:<br>Warning: 1-4 interaction ... your system is exploding<br><br>it says modifying interaction tables!<br>
<br>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!<br><br>Thanks in advance for your reply<br><br><br><br><br><br><br><div class="gmail_quote">On Sun, Apr 3, 2011 at 8:33 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">On 4/04/2011 1:51 AM, mohsen ramezanpour wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear All<br>
<br>
I have a file which contains afew residues (noncontinuous),<br>
When I use mdrun on a computer(4 cpu) I am facing with the following Error:<br>
<br>
Fatal error:<br>
There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 3.28697 nm<br>
Change the number of nodes or mdrun option -rdd<br>
Look in the log file for details on the domain decomposition<br>
<br>
<br>
it is relating to domain decomposition,<br>
Besides I checked either restraining residues and not restraining.But it dosn't differed<br>
<br>
I changed the number of nodes to 1 but it didn't work!<br>
mpirun -np 1 mdrun -v -deffnm EM<br>
<br>
Besides I looked in the log file and the important part of it was:<br>
<br>
Initializing Domain Decomposition on 4 nodes<br>
Dynamic load balancing: no<br>
Will sort the charge groups at every domain (re)decomposition<br>
Initial maximum inter charge-group distances:<br>
two-body bonded interactions: 2.988 nm, LJ-14, atoms 922 943<br>
multi-body bonded interactions: 2.988 nm, Proper Dih., atoms 922 943<br>
Minimum cell size due to bonded interactions: 3.287 nm<br>
Using 0 separate PME nodes<br>
Optimizing the DD grid for 4 cells with a minimum initial size of 3.287 nm<br>
The maximum allowed number of cells is: X 1 Y 1 Z 1<br>
<br>
<br>
please let me know how can I solve this problem.<br>
Thanks in advance<br>
</blockquote>
<br></div></div>
Why do you have bonds nearly 3nm long?<br>
<br>
Mark<br><font color="#888888">
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