[AMBER] Query for umbrella sampling

From: Saikat Pal <saikatpaliitg.yahoo.com>
Date: Wed, 12 Sep 2018 20:36:57 +0000 (UTC)

Sent from Yahoo Mail on Android
 
   ----- Forwarded message ----- From: "Saikat Pal" <saikatpaliitg.yahoo.com> To: "AMBER Mailing List" <amber.ambermd.org> Cc: Sent: Wed, 12 Sep 2018 at 12:39 PM Subject: Query for umbrella sampling Dear all,I want to calculate the PMF of two peptides. I want to pull two atoms along the Z axis. I want to know is my input is correct or not ?:4000 step minimization for 15 ang
#minimisation
 &cntrl
  imin = 1,
  maxcyc=4000, ncyc = 1000,
  ntpr = 100, ntwr = 1000,
  ntf = 1, ntc = 1, cut = 10.0,
  ntb = 1, ntp = 0,
  nmropt = 1,
 &end
 &wt
  type='END',
 &end
DISANG=disang.15

#equilibration1000 ps NPT equilibration for 15 ang
 &cntrl
  imin = 0, ntx = 1, irest = 0,
  ntpr = 5000, ntwr = 50000, ntwx = 0,
  ntf = 2, ntc = 2, cut = 10.0,
  ntb = 2, nstlim = 500000, dt = 0.002,
  tempi=0.0, temp0 = 298.0, ntt = 3,
  gamma_ln = 1.0,
  ntp = 1, pres0 = 1.0, taup = 5.0,
  nmropt = 1, ioutfm=1,
 &end
 &wt
  type='END',
 &end
DISANG=disang.15

#production10 ns NPT production for 15 ang
 &cntrl
  imin = 0, ntx = 5, irest = 1,
  dielc=1.0,cut=10.0,
  ntt=1,temp0=298.0,tautp=0.1,
  ntp=1,ntb=2,ntc=2,ntf=2,
  iwrap=1,nstlim=5000000,dt=0.002,
  ntwx=1000,ntpr=500,nmropt=1,
  pres0 = 1.0,
 &end
 &wt
  type='DUMPFREQ', istep1=10,
 &end
 &wt
  type='END',
 &end
DISANG=disang.15
DUMPAVE=distance_15.dat

#disang#Harmonic restraints for 15 ang
 &rst
  iat=-1,-1,
  iresid=1,
  r1=-99.00000, r2=15.00000, r3=15.00000, r4=99.00000,
  rk2=6.0, rk3=6.0,
  igr1=6,0,
  igr2=1,1,0,
  grnam1(1)='O14',
  grnam2(1)='N1',grnam2(2)='N3',
 /
         

 

Thanks and Regards,
Saikat Pal



  
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 12 2018 - 14:00:02 PDT
Custom Search