[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
> At 2011-12-31 04:42:12,"Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at vt.edu>> wrote:
>>> Dear Justin Lemkul,
>>> I find a tutorial about the free energy calculation by g_bar in
>>> Gromacs. (
>>> 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:
> 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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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