[gmx-users] too much warnings and notes

[Carsten Kutzner]

Hi,

find the reason for the warnings in your mdp file settings
and adjust them accordingly.

You can also override the warnings with the -maxwarn <number>
option in grompp.

Carsten



On Oct 29, 2012, at 3:52 PM, Albert <mailmd2011 at gmail.com> wrote:

> 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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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner