[gmx-users] Position Restraints MD

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jan 29 00:11:55 CET 2008

Philip Shushkov wrote:
> Dear Mark,
> I have checked this possibility and it turned out that the positional 
> restraints and constraints did not lead to MD instabilities when run in 
> serial mode. Unfortunately, the system is pretty large (it consists of 
> 27255 atoms) so it runs quite slowly in serial mode. That is why, I do 
> want to run mdrun in parallel mode and make an advantage of our cluster. 
> Thus, I would like to ask you for some advice how to get around the problem.

OK, well to do this you need to identify the actual source of problems. 
Try simplifying your chemical system somehow, and/or changing which 
parts of it have constraints and/or restraints. You should also be 
describing to us what your system contains, and where the LINCS errors 
were occuring, else we're guessing in the dark.


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