Hi all,
I want to model a short cyclic peptide (10 residues) with a POPC bilayer.
I adapted & modified the input files originating from the tutorial
“
Lipid 128 heating 100K
&cntrl
imin=0,
ntx=1,
irest=0,
ntc=2,
ntf=2,
tol=0.0000001,
nstlim=2500,
ntt=3,
gamma_ln=1.0,
ntr=1,
ig=-1,
ntpr=100,
ntwr=10000,
ntwx=100,
dt=0.002,
nmropt=1,
ntb=1,
ntp=0,
cut=10.0,
ioutfm=1,
ntxo=2,
/
&wt
type='TEMP0',
istep1=0,
istep2=2500,
value1=0.0,
value2=100.0 /
&wt type='END' /
Hold lipid fixed
10.0
RES 1 893
END
END
“
But however, it does not seem to work. I have run a short MD run on both the peptide and bilayer apart, prior to combining them using xleap.
The error given back is :
Error: an illegal memory access was encountered launching kernel kClearForces
cudaFree GpuBuffer::Deallocate failed an illegal memory access was encountered
But I guess this is not saying much.
This is the outcome of the Minimalization step:
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
5249 -1.7686E+05 8.1124E-01 1.3333E+02 H2 69725
BOND = 11896.5815 ANGLE = 3134.1516 DIHED = 10309.9775
VDWAALS = 16903.7553 EEL = -217213.3077 HBOND = 0.0000
1-4 VDW = 3511.3187 1-4 EEL = -5398.5000 RESTRAINT = 0.0000
Any suggestions?
Vic De Roo
PhD Student
NMRSTR Group<
https://www.ugent.be/we/orgchem/nmr-structure-analysis/en>
Department of Organic and Macromolecular Chemistry
Krijgslaan 281, S4-bis, 1st floor
B-9000 GENT
Belgium
+32456123894
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Received on Mon Feb 14 2022 - 01:30:02 PST
