[gmx-users] npt.tpr protein-lig

[Iman Katouzian]

Good day,

I have generated npt.tpr for my protein ligand and changed my npt.mdp file
according to the suggestions by GROMACS for using Brendsen and h-bonds for
constraints finally I encounter this NOTE which I think will cause further
problems in my md run :
 NOTE 1 [file topol.top, line 18260]:
  The bond in molecule-type UNL between atoms 6 C5 and 7 C6 has an
  estimated oscillational period of 1.8e-02 ps, which is less than 10 times
  the time step of 2.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.

Number of degrees of freedom in T-Coupling group Protein_UNL is 4960.82
Number of degrees of freedom in T-Coupling group Water_and_ions is 77850.18
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm

I would appreciate it if someone tells me what I need to do with my system
I think it may be related to the time step of my simulaiton and frames as I
searched the similar issues.

thanks

-- 

*Iman Katouzian*

*Ph.D.** candidate of Food Process Engineering*

*Faculty of Food Science and Technology*

*University of Agricultural Sciences and Natural Resources, Gorgan, Iran*