Umbrella sampling with Amber

AMBER tutorial for bond torsion sampling: https://ambermd.org/tutorials/advanced/tutorial17/

 

WHAM program: http://membrane.urmc.rochester.edu/?page_id=126

 

Path (in Cosmos) to Iria's files: /lunarc/nobackup/projects/teobio/Iria/DMA-DCM

 

Example of WHAM input file and "successful" WHAM output file (in Cosmos): /home/iria/lu2023-17-25/amber_2/umbrella/DMA-DCM/WHAM

 

Example for executing wham: 
wham 6.1 30.0 100 0.000001 300 0 input result.out

wham [P|Ppi|Pval] hist_min hist_max num_bins tol temperature numpad  \
        metadatafile freefile [num_MC_trials randSeed]

Input file to wham (file name, restraint, force constant = 2*Amber force constant)
D_6.2.dat 6.2 20
D_6.3.dat 6.3 20
D_6.4.dat 6.4 20
D_6.5.dat 6.5 20
D_6.6.dat 6.6 20
D_6.7.dat 6.7 20
D_6.9.dat 6.9 20
...
Sample WHAM output file (energies are in kcal/mol):


#Coor           Free    +/-             Prob            +/-
6.214875        3.786040        nan     0.000005        nan
6.244625        3.698232        nan     0.000006        nan
6.274375        3.582968        nan     0.000008        nan
...

29.925625       0.000000        nan     0.003238        nan
29.955375       0.018200        nan     0.003140        nan
29.985125       0.021748        nan     0.003121        nan
#Window         Free    +/-    
#0      0.000000        nan
#1      -0.355987       nan
#2      -0.639687       nan
#3      -0.871719       nan

...


Iria's five sander.in files:

sander.in1

Minimisation without shake.
 &cntrl
  irest=0,ntx=1,
  nstlim=0,dt=0.0005,
  imin=1,maxcyc=1000,drms=0.001,
  temp0=300.0,ntt=3,gamma_ln=2.0,
  ntc=1,ntf=1,
  nsnb=40,cut=8.0,dielc=1.0,
  ntpr=100,ntwx=0,ntwv=0,ntwe=0,iwrap=1,ioutfm=0,ntxo=1,
  ntb=1,ntp=0,taup=0.2,
  ipol=0,igb=0,
  ncyc=10,ntmin=1,dx0=0.01,
 &end
 &wt
  type='END',
 &end


sander.in2
10 ps MD simulation without shake
&cntrl
  irest=0,ntx=1,
  nstlim=20000,dt=0.0005,
  imin=0,maxcyc=100,drms=0.001,
  temp0=300.0,ntt=3,gamma_ln=2.0,
  ntc=1,ntf=1,
  nsnb=40,cut=8.0,dielc=1.0,
  ntpr=1000,ntwx=0,ntwv=0,ntwe=0,iwrap=1,ioutfm=0,ntxo=1,
  ntb=1,ntp=0,taup=0.2,
  ipol=0,igb=0,
  ncyc=10,ntmin=1,dx0=0.01,
  nmropt = 1,
 &end
&wt
  type='END',
&end
DISANG=dist.RST
LISTIN=POUT
LISTOUT=POUT


sander.in3

1 ns NVT equilibration with shake and constant volume
 &cntrl
  irest=1,ntx=5,
  nstlim=500000,dt=0.002,
  temp0=300.0,ntt=3,gamma_ln=2.0,
  ntc=2,ntf=2,
  nsnb=15,cut=8.0,dielc=1.0,
  ntpr=10000,ntwx=10000,ntwv=0,ntwe=0,iwrap=1,ioutfm=0,ntxo=1,
  ntb=1,ntp=0,taup=0.2,
  ipol=0,igb=0,
  nmropt = 1,
 &end
 &wt
  type='END',
 &end
DISANG=dist.RST


sander.in4

1 ns  npT equilibration with shake
 &cntrl
  irest=1,ntx=5,
  nstlim=500000,dt=0.002,
  temp0=300.0,ntt=3,gamma_ln=2.0,
  ntc=2,ntf=2,
  nsnb=15,cut=8.0,dielc=1.0,
  ntpr=1000,ntwx=5000,ntwv=-1,ntwe=0,iwrap=1,ioutfm=1,ntxo=1,
  ntb=2,ntp=1,pres0=1.0,taup=1.0,
  ipol=0,igb=0,
  nmropt=1, ioutfm=1,
 &end
 &wt
  type='DUMPFREQ', istep1=1000,
 &end
 &wt
  type='END',
 &end
DISANG=dist.RST
DUMPAVE=dist_5.dat
LISTIN=POUT
LISTOUT=POUT


sander.in5

10 ns  npT production with shake
 &cntrl
  irest=1,ntx=5,
  nstlim=5000000,dt=0.002,
  temp0=300.0,ntt=3,gamma_ln=2.0,
  ntc=2,ntf=2,
  nsnb=15,cut=8.0,dielc=1.0,
  ntpr=1000,ntwx=5000,ntwv=-1,ntwe=0,iwrap=1,ioutfm=1,ntxo=1,
  ntb=2,ntp=1,pres0=1.0,taup=1.0,
  ipol=0,igb=0,
  nmropt=1, ioutfm=1,
 &end
 &wt
  type='DUMPFREQ', istep1=1000,
 &end
 &wt
  type='END',
 &end
DISANG=dist.RST
DUMPAVE=dist_final.dat
LISTIN=POUT
LISTOUT=POUT


The dist.RST file
&rst iat=46,96, r1=-99.0, r2=6.1, r3=6.1, r4=99.0, rk2=10, rk3=10, iresid=0, outxyz=1, /


The dist_final.dat file
       0     x:    1.903    y:    -5.660    z:     2.048        6.313
    1000     x:    2.321    y:    -5.565    z:     1.284        6.165
    2000     x:    1.900    y:    -5.994    z:     1.196        6.400
    3000     x:    1.600    y:    -5.983    z:     0.773        6.241
    4000     x:    1.119    y:    -5.681    z:     1.969        6.116
...

 4997000     x:    3.762    y:    -4.029    z:     3.080        6.314
 4998000     x:    3.952    y:    -4.173    z:     3.027        6.495
 4999000     x:    3.892    y:    -4.119    z:     2.743        6.296