Dear all,
I am using AMBER12 (pmemd.cuda.MPI) and I used the following input file:
run: step 1 MD
&cntrl
imin = 0,
irest = 0 ,
ntx = 1,
nstlim = 5000, dt = 0.002,
ntc = 2 , ntf = 2,
ntt = 3, gamma_ln = 2.0,
ntp=1, taup=1,
pres0=1,
tempi = 100.0, temp0 =100.0,
ntb = 2 ,
ntpr = 250 , ntwx = 250, ntwr = 500 ,
cut = 9,
ioutfm = 1
ntr=1
&end
Keep DNA fixed with weak restraints
8000.0
RES 1 136
END
END
and the calculation ends with the following error:
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
----- READING GROUP 1; TITLE:
Keep DNA fixed with weak restraints
GROUP 1 HAS HARMONIC CONSTRAINTS 8000.00000
GRP 1 RES 1 TO 136
Number of atoms in this group = 1604
----- READING GROUP 2; TITLE:
END
rfree: End of file on unit 5
In my job, I used these commands:
cmd="pmemd.cuda.MPI -O -i step1.in -o dimero_step1.out -p
dimero_spce.prmtop -c dimero_spce.
inpcrd -r dimero_step1.rst -x dimero_step1.mdcrd -ref dimero_spce.inpcrd"
export CUDA_NIC_INTEROP=1
mpirun -np 4 $cmd
Thank you in advance
Elisa
--
Elisa Frezza
Ph.D. Student in Materials Science and Engineering
Dipartimento di Scienze Chimiche
Università di Padova
via Marzolo, 1
35131 Padova - Italy
Phone: +39 049 827 5149
Skype: elisa.frezza
Emai: elisa.frezza.gmail.com
elisa.frezza.studenti.unipd.it
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Received on Thu Oct 11 2012 - 07:00:04 PDT
