[gmx-users] protein with ions

[Justin Lemkul]

On 6/26/18 12:42 PM, Владимир Богданов wrote:
> Hey everyone!
> Could you help me please?
> When I make md.tpr file I get this note:
> gmx_mpi grompp -f md.mdp -c npt.gro -r npt.gro -n index.ndx -t npt.cpt 
> -p topol.top -o md.tpr
> Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
> Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps'
> Setting the LD random seed to 943784487
> Generated 330891 of the 330891 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 330891 of the 330891 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'Ion_chain_A2'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
> turning all bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning all bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'NA'
> turning all bonds into constraints...
> Removing all charge groups because cutoff-scheme=Verlet
> NOTE 1 [file topol.top, line 51]:
>   In moleculetype 'Ion_chain_A2' 4 atoms are not bound by a potential or
>   constraint to any other atom in the same moleculetype. Although
>   technically this might not cause issues in a simulation, this often 
> means
>   that the user forgot to add a bond/potential/constraint or put multiple
>   molecules in the same moleculetype definition by mistake. Run with -v to
>   get information for each atom.
> Number of degrees of freedom in T-Coupling group SOL is 62364.00
> Number of degrees of freedom in T-Coupling group not_SOL is 5300.00
> Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 315 K
> Calculated rlist for 1x1 atom pair-list as 1.299 nm, buffer size 0.099 nm
> Set rlist, assuming 4x4 atom pair-list, to 1.226 nm, buffer size 0.026 nm
> Note that mdrun will redetermine rlist based on the actual pair-list setup
> Reading Coordinates, Velocities and Box size from old trajectory
> Will read whole trajectory
> Last frame         -1 time 2000.000
> Using frame at t = 2000 ps
> Starting time for run is 0 ps
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 60x60x60, spacing 0.116 0.116 0.116
> Estimate for the relative computational load of the PME mesh part: 0.23
> NOTE 2 [file md.mdp]:
>   This run will generate roughly 2063 Mb of data
> There were 2 notes
> Back Off! I just backed up md.tpr to ./#md.tpr.1#
> GROMACS reminds you: "Your Country Needs YOU" (U.S. Army)
> Is this ok for my simulation? I do MD of calmodulin and ions of CA 
> (molecule type 'Ion_chain_A2') is important for my system.

grompp is simply trying to make you aware that you're doing something 
unusual. Apparently you're relying simply on nonbonded interactions to 
maintain the poses of the bound Ca2+. You should scrutinize your chosen 
force field's history to understand whether or not that's a reliable 
approach. Ion coordination often includes some type of distance 
restraint to account for inaccuracies in nonbonded potentials.

-Justin

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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