[AMBER] problem restraint

From: Elisa Frezza <elisa.frezza.gmail.com>
Date: Thu, 11 Oct 2012 15:53:45 +0200

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
UniversitÓ 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
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