[gmx-users] problem of umbrella sampling pulling code

Albert mailmd2011 at gmail.com
Fri Apr 5 20:03:55 CEST 2013


  I am trying to run umbrella sampling, the system contains a ligand. 
here is the pulling setting:

; Pull code
pull            = umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim        = Y N N
pull_start      = yes       ; define initial COM distance > 0
pull_ngroups    = 1
pull_group0     = Protein
pull_group1     = LIG
pull_rate1      = 0.001      ; 0.01 nm per ps = 10 nm per ns
pull_k1         = 1000      ; kJ mol^-1 nm^-2

I am trying to run with command:

grompp -f md_pull.mdp -c npt.gro -p complex.top -n index.ndx -o pull.tpr

but it failed with messages:

The center of mass of the position restraint coord's is  4.491 3.784  3.540
Pull group 0 'Protein' has 4661 atoms
Pull group 1 'LIG' has 30 atoms
Number of degrees of freedom in T-Coupling group Protein_LIG is 9315.71
Number of degrees of freedom in T-Coupling group Water_and_ions is 85476.30
Largest charge group radii for Van der Waals: 5.945, 5.940 nm
Largest charge group radii for Coulomb:       5.954, 5.951 nm

WARNING 1 [file md_pull.mdp]:
   The sum of the two largest charge group radii (11.905330) is larger than
   rlist (1.200000)

Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 80x64x60, spacing 0.112 0.118 0.118
Pull group  natoms  pbc atom  distance at start     reference at t=0
        0      4661      2331
        1        30      4676   0.682 0.682
Estimate for the relative computational load of the PME mesh part: 0.17
This run will generate roughly 906 Mb of data

There was 1 note

There was 1 warning

Program grompp, VERSION 4.5.5
Source code file: grompp.c, line: 1584

Fatal error:
Too many warnings (1), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

"Just Give Me a Blip" (F. Black)

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