[gmx-users] umbrella sampling; PMF, pull.pdo and g_wham

Sekwan Oh ohsk75 at stanford.edu
Tue Aug 24 01:50:17 CEST 2004

Dear gromacs users,

I've tried to calculate PMF by stretching polypeptide using umbrella 
sampling, and obtained a 'pull.pdo' file.

I have two questions,

However I don't know how should I deal with this file. I got the error 
messages when I ran 'g_wham' as follows,

%g_wham pull.pdl  [Enter]

                                 :-)  g_wham  (-:

Option     Filename  Type         Description
   -o    profile.xvg  Output       xvgr/xmgr file
-hist     histo.xvg  Output       xvgr/xmgr file

       Option   Type  Value  Description
       -[no]h   bool     no  Print help info and quit
        -nice    int      0  Set the nicelevel
       -[no]w   bool     no  View output xvg, xpm, eps and pdb files
         -min   real      0  Minimum coordinate in profile
         -max   real      0  Maximum coordinate in profile
        -bins    int    100  Number of bins in profile
    -[no]prof   bool    yes  Only calculate min and max
        -temp   real    298  Temperature
    -[no]flip   bool     no  Combine halves of profile
         -tol   real   0.01  Tolerance

Opening file pull.pdo.

gunzip: stdin: not in gzip format
Fatal error: This does not appear to be a valid pdo file

Why do we get this Fatal error?

The way I stretched this single 20-mer polypeptide is setting "one atom in 
one-end as a reference group" and "the other atom in the other end of the 
peptide to be pulled".

The pull.ppa is as follows,
verbose = yes
runtype = umbrella
group_1 = A
reference_group = B
reftype = com
reflag = 1
Skip steps = 10
pulldim = Y Y Y
k1 = -500

After the simulation finished, I tried to obtain the energies of the 
polypeptide using 'g_energy'.
However there was no 'G96bond' energy on the list and G96Angle starts first 

    1=      G96Angle   2=   Proper Dih.   3= Improper Dih.   4=         LJ-14
    5=    Coulomb-14   6=       LJ (SR)   7=       LJ (LR)   8=  Coulomb (SR)
    9=  Coulomb (LR)  10=Position Rest.  11=     Potential  12=   Kinetic En.
   13=  Total Energy  14=   Temperature  15=Pressure (bar)  16=        Vir-XX
   17=        Vir-XY  18=        Vir-XZ  19=        Vir-YX  20=        Vir-YY
   21=        Vir-YZ  22=        Vir-ZX  23=        Vir-ZY  24=        Vir-ZZ
   25= Pres-XX (bar)  26= Pres-XY (bar)  27= Pres-XZ (bar)  28= Pres-YX (bar)
   29= Pres-YY (bar)  30= Pres-YZ (bar)  31= Pres-ZX (bar)  32= Pres-ZY (bar)
   33= Pres-ZZ (bar)  34= #Surf*SurfTen  35=          Mu-X  36=          Mu-Y
   37=          Mu-Z  38=Coul-SR:Protein-Protein  39=LJ:Protein-Protein 
   41=LJ-LR:Protein-Protein  42=Coul-14:Protein-Protein 

Why is this happeing?

Any helps will be greatly appreciated.



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