Dear Amber users,
I try to run sander (Amber12) on several processors with following
parameters:
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 8.0, ntr = 0,
ntc = 2, ntf = 2,
tempi = 310.0, temp0 = 310.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 500000, dt = 0.002,
ntpr = 500, ntwx = 500, ntwr = 1000
/
but I have an error message, if I choose more than 8 processors:
partition error in shake on processor 0
this processor has atoms 1 through 12072
atom 12072 is within this range
atom 12073 is not within this range !
My system consist of glycosylated protein and two ligand molecules in
explicit water, atom 12072 is a carbon and 12073 is a hydrogen of first
ligand.
Could you please help me to fix it.
Sincerely yours,
Evgenia.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 26 2015 - 07:00:02 PDT
