[gmx-users] problem of umbrella sampling pulling code

[Justin Lemkul]

On Fri, Apr 5, 2013 at 2:03 PM, Albert <mailmd2011 at gmail.com> wrote:

> Hello:
>
>  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<http://www.gromacs.org/Documentation/Errors>
> ------------------------------**-------------------------
>
> "Just Give Me a Blip" (F. Black)
>
>
You either have massive charge groups (i.e. a bad topology) or your
molecules are broken across periodic boundaries (which would be the case if
the charge group size was roughly equivalent to the size of one of your box
vectors).

-Justin

-- 

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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