hello:
I am generating a .tpr file for proten/ligand system, but it has so
much warnings:
NOTE 1 [file md.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 2 [file md.mdp]:
leapfrog does not yet support Nose-Hoover chains, nhchainlength reset
to 1
Generated 23436 of the 23436 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 20254 of the 23436 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'LIG'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'POPC'
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...
Excluding 1 bonded neighbours molecule type 'CL'
turning all bonds into constraints...
Setting gen_seed to 6947582
Velocities were taken from a Maxwell distribution at 300 K
NOTE 3 [file complex.top]:
The largest charge group contains 12 atoms.
Since atoms only see each other when the centers of geometry of the
charge
groups they belong to are within the cut-off distance, too large charge
groups can lead to serious cut-off artifacts.
For efficiency and accuracy, charge group should consist of a few atoms.
For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
Number of degrees of freedom in T-Coupling group Protein_LIG is 9475.34
Number of degrees of freedom in T-Coupling group POPC is 33353.66
Number of degrees of freedom in T-Coupling group Water_and_ions is 53973.00
Largest charge group radii for Van der Waals: 0.299, 0.299 nm
Largest charge group radii for Coulomb: 0.299, 0.299 nm
NOTE 4 [file md.mdp]:
The sum of the two largest charge group radii (0.597592) is larger than
rlist (1.000000) - rvdw (1.200000)
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