Hi, I don't know why I get the following error message when I use more than one node when I run grompp (e.g., grompp -np 32 .....). From previous emails, I gathered that I need to reduce the number of nodes. But for me it just works when I use a single node.
Any suggestions? Cheers, Siavoush
Here is the error:
Walking down the molecule graph to make shake-blocks
There are 556 charge group borders and 1 shake borders
There are 556 total borders
Division over nodes in atoms:
41 41 42 40 42 42 44 41 42
41 42 42 42 41 42 40 43 42 41
41 41 42 40 41 42 40 41 37 42
43 41 42
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: splitter.c, line: 121
Fatal error:
Shake block crossing node boundaries
constraint between atoms (1270,1283)
-------------------------------------------------------
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