AMBER Archive (2008)

Subject: AMBER: NMR restraints

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Mon Apr 28 2008 - 01:53:51 CDT

Dear AMBER users,

For testing the nmropt=1 option of AMBER9, I have the following input
file:
--------------- md.in -----------------------
1 ns simulation with lambda = 0.45 - Production
 &cntrl
  imin=0,
  ntx=5,irest=1,
  ntpr=50,ntwr=50,ntwx=1000,
  ntc=2,ntf=2,ntb=1,cut=8,nmropt=1,
  noshakemask = '@%DH | (@%H & !@H1)',
  ntr=0,
  nstlim=1000000,dt=0.001,nscm=5000,nrespa=1,
  ntt=3,gamma_ln=1,tempi=300,temp0=300,ig=233,
  ntp=0,taup=2.0,pres0=1,
  icfe=2,klambda=6,clambda=0.45
 /
 &wt type='REST', istep1=0,istep2=50000,value1=1.0,
             value2=1.0, /
 &wt type='END' /
LISTOUT=POUT
DISANG=/tmp/yildirim/ggcc_ss_expl_a9_NMR/l_0.45/RST
-----------------------------------------------

>From step=0 to step=50000, the REST is set to 1. In the output file, for
steps > 50000, I still see RESTRAINT energies. Is this normal? Thanks. 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  = Department of Physics        -                              =
  = University of Rochester      -                              =
  = 585-275-6766 (office)        - 585-267-5644 (home)          =
  = http://www.pas.rochester.edu/~yildirim/                     =
  ---------------------------------------------------------------

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