Im trying to refine an nmr structure using our new GPU/pmemd.cuda.
I just brought over all the input files i used for sander which is
simulated annealing protocol, 30
ps
&cntrl
nstlim=30000, pencut=-0.01,
nmropt=1,
ntpr=200, ntt=1,
ntwx=200,
cut=999.0, ntb=0,
rgbmax=16,
igb=1,
saltcon=0.2,
/
&ewald
/
#
#Simple simulated annealing
algorithm:
#
#from steps 0 to 5000: heat the system to
600K
#from steps 5001-18000: re-cool to low temperatures with long
tautp
#from steps 18001-20000: final cooling with short
tautp
#
&wt type='TEMP0',
istep1=0,istep2=3000,value1=10.0,
value2=1000.,
/
&wt type='TEMP0', istep1=3001, istep2=8000,
value1=1000.0,
value2=1000.0,
/
&wt type='TEMP0', istep1=8001, istep2=30000,
value1=0.0,
value2=0.0,
/
&wt type='TAUTP',
istep1=0,istep2=8000,value1=0.2,
value2=0.2,
/
&wt type='TAUTP',
istep1=8001,istep2=24000,value1=4.0,
value2=2.0,
/
&wt type='TAUTP',
istep1=24001,istep2=27000,value1=1.0,
value2=1.0,
/
&wt type='TAUTP',
istep1=27001,istep2=29000,value1=0.5,
value2=0.5,
/
&wt type='TAUTP',
istep1=29001,istep2=30000,value1=0.05,
value2=0.05,
/
&wt type='REST',
istep1=0,istep2=8000,value1=0.1,
value2=1.00,
/
&wt type='REST',
istep1=8001,istep2=30000,value1=1.00,
value2=1.00,
/
&wt type='END'
/
LISTOUT=POUT
DISANG=RST
Upon submission i get STOP PMEMD Terminated Abnormally!
Looking at the output i get the following error.
Implicit solvent radii are modified Bondi radii
(mbondi)
CUDA (GPU): Implementation does not currently support the use of COM
simulations.
Require iat(2) >= 0.
I think this has to do with my restraint file but im not sure what to fix.
Thanks foryou help.
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Received on Wed Sep 19 2012 - 14:00:03 PDT
