I am trying to run dynamics of DNA oligo ( 11 mer) with explicit water
molecules ( about 3000 molecules).
Shake routine is :
shake
reference = parameters
bonds (hydrogen) (all)
tolerance = 1.0e-06
nconstraints=8000
end
and error message after this is:
**********************************
X-PLOR>shake
SHAKE> reference = parameters
SHAKE> bonds (hydrogen) (all)
SELRPN: 7142 atoms have been selected out of 11032
SELRPN: 11032 atoms have been selected out of 11032
SHKSET: reference = parameters
%XREFIN-ERR: allocation for SHAKE-constraints exceeded
increase NCON parameter and run again
%XREFIN>-ERR: exceeded allocation for SHAKE-constraints
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
BOMLEV= 0 reached. Program execution will be terminated.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Subroutine DIE called . Terminating
Supposedly, I have 7142 hydrogen atoms and only constraints which SHAKE
routine will take into consideration is bonds between hydrogen and heavy
atoms, no more then 7142 .
I tried 8000, 30000, 600000...
Sours code didn't give me any limitation for this parameter, it should
be integer, it is not limited. What is wrong with it?
Can somebody give me any advise? Thank you all, Tanya Zaliznyak.
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