[gmx-users] Re: Hi, May I ask you a question about the free energy calculation tutorial?

Justin A. Lemkul jalemkul at vt.edu
Sun Jan 1 06:25:13 CET 2012

yywang wrote:
> At 2011-12-31 04:42:12,"Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at vt.edu>> wrote:
>>yywang wrote:
>>>  Dear Justin Lemkul,
>>>          I find a tutorial about the free energy calculation by g_bar in 
>>> Gromacs.  (  
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html)
>>>          I have a question when I use this tutorail. That is I cannot 
>>> use muti-cores in cluster. When I try to use mpirun -np 2 or more, an 
>>> error occured (There is no domain decomposition for 2 nodes that is 
>>> compatible with the given box and a minimum cell size of 6.46036 nm 228 
>>> Change the number of nodes or mdrun option -rdd)
>>>  But when i turn the mpirun off ,eg mpirun -np 1 mdrun -nt 2 ,  
>>> everything is OK.
>>I do not know the basis for why MPI vs. threading would lead to different 
>>behavior.  I use threading by default on a dual-core machine since the tutorial 
>>system is small.
>>>          Since my model is a little big, the speed of use 1 core and 2 
>>> threads is too slow, is there any method to change this situation, or do 
>>> you know any paramater that control this?
>>Are we still talking about the tutorial system?  It is quite small.  The DD cell 
>>size you've posted above seems to be from a different system.  I cannot offer 
>>personalized advice for individual systems that I've not worked with.  The best 
>>information is online:
>  >http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm
> Sorry I haven`t express my idea well. I use your tutorial to calculation the free energy of a big system of my own,which is a big system of 24,0000 atoms, so this speed is too slow for me and I am trying to run it on big clusters.
> Thanks any way.

The simple decoupling procedure in the tutorial is likely not suitable for very 
large systems; by changing many degrees of freedom simultaneously in this way, 
convergence is exceptionally hard to achieve.  I suspect the very large size of 
the DD cells is related to the couple-intramol parameter, which for large 
systems results in explicit pair interactions, which occur within the same DD 
cell.  Refer to the manual for a more suitable setting and the reasons why you 
might want to adjust certain parameters.  Good luck.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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