Moeed wrote:
Hello Justin,
I am running in parallel but this error comes up with 8, 7, 6, 5, 4 and
even 3 number of processors. I read about domain decomposition on the
website and tried less number of processors, as just mentioned. My
understanting after reading about the error is that parallel simulation
is not working with a small system as mine! but there are 11000 atoms in
there and I am doing FE stuff... I dont see why this is considered as
small simulation!
This exact situation was just discussed last week regarding FEP and DD (hint:
check the archive!). If you set your intramolecular interactions to be computed
as exclusions and pairs (i.e. couple_intramol=no), then you have (essentially)
long-range bonded interactions. Either use mdrun -pd or run in serial.
=============================
There is no domain decomposition for 4 nodes that is compatible with the
given box and a minimum cell size of 5.70044 nm
Change the number of nodes or mdrun option -rdd or -dds
=========================
Also I checked the manual for the options below but I have no clue what
value to set for my system.
-rdd real 0 The maximum distance for bonded interactions
with
DD (nm), 0 is determine from initial coordinates
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
***************************************
Thanks,
Moeed
BTW: About mdp setting for electrostatics, I have set zero charges to
all atoms so there is no electrostatics term ( I have only C and H).
Thats why I commented out ;coulombtype = PME
For both solute and solvent? Just one? Seems like an unreasonable model to me.
Even hydrocarbons should have some (obviously offsetting) partial charge.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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