[gmx-users] Re : Unable to generate umbrella histogram and PMF curve

[Norfarisha Mohd Fadil]

Dear Justin,


 I have checked the log file for the particular xvg file and found that there's no simulation (?) being ran as compared to the other log files that generated the force profile for their respective xvg files. The info I have obtained are as below. So what should I do next? Should I recompile again with grompp command for that particular tpr file and run the umbrella sampling simulation again?


Will do ordinary reciprocal space Ewald sum.
Using a Gaussian width (1/beta) of 0.448228 nm for Ewald
Cut-off's:   NS: 1.435   Coulomb: 1.4   LJ: 1.4
Long Range LJ corr.: <C6> 3.3659e-04
System total charge: 0.000
Generated table with 1217 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1217 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 1217 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 1217 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1217 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1217 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Potential shift: LJ r^-12: -1.764e-02 r^-6: -1.328e-01, Ewald -1.000e-05
Initialized non-bonded Ewald correction tables, spacing: 1.10e-03 size: 1270


Using AVX2_256 4x8 non-bonded kernels

Using full Lennard-Jones parameter combination matrix

Removing pbc first time
Pinning threads with an auto-selected logical core stride of 1

Will apply potential COM pulling
with 1 pull coordinate and 3 groups
Pull group 1:   226 atoms, mass  2617.110
Pull group 2:   226 atoms, mass  2617.110

Initializing LINear Constraint Solver

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------

The number of constraints is 1135

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------

Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest
There are: 33207 Atoms

Constraining the starting coordinates (step 0)

Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 4.06e-05
Initial temperature: 310.709 K

Started mdrun on rank 0 Sun Jun 18 16:09:16 2017
           Step           Time         Lambda
              0        0.00000        0.00000

   Energies (kJ/mol)
       G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    1.71377e+03    6.94317e+02    6.05464e+02   -1.93216e+02    2.40046e+04
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
    7.17270e+04   -1.62629e+03   -5.69892e+05    1.04745e+03    7.66548e-03
   COM Pull En.      Potential    Kinetic En.   Total Energy    Temperature
    2.24400e-12   -4.71919e+05    8.67853e+04   -3.85133e+05    3.14119e+02
 Pres. DC (bar) Pressure (bar)   Constr. rmsd
   -7.75857e+01    7.06903e+01    2.15112e-05




Best regards,


Norfarisha binti Mohd Fadil

Student

Department of Chemistry
Faculty of Science
UTM, Johor Bahru
Malaysia

Phone: +6011-26651278