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

[Justin Lemkul]

On 6/19/17 10:57 PM, Norfarisha Mohd Fadil wrote:
> 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?
> 

You don't need to recreate the .tpr, just run the simulation over again. 
Something failed but there's no indication as to what (queue problem, hardware, 
etc).

-Justin

> 
> 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
> 

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================