Thank you for your replies, it helps me a lot.
Now I’m performing double system-single box simulation for I2M mutation. The system consisted of the folded_wt (I2M) and unfolded_mutant (tripeptide M2I) separated at least 3 nm which solvated and neutralized in a dodecahedron box.
I generated the ACE-GLY-MET-GLY-NME capped tripeptide using tleap program and amber99sb-star-ildn force field.
I do use the python 3 pmx ‘develop’ branch to mutate both the folded_wt and unfolded_mutant pairs. However, I always face these warnings and notes during nvt, npt, and equilibirum simulations:
WARNING 1 [~/dssb_mdp/eqA/nvt-A.mdp, line 62]:
You are using soft-core interactions while the Van der Waals interactions
are not decoupled (note that the sc-coul option is only active when using
lambda states). Although this will not lead to errors, you will need much
more sampling than without soft-core interactions. Consider using
NOTE 1 [file ~/dssb_mdp/eqA/nvt-A.mdp]:
With PME there is a minor soft core effect present at the cut-off,
proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on
energy conservation, but usually other effects dominate. With a common
sigma value of 0.34 nm the fraction of the particle-particle potential at
the cut-off at lambda=0.5 is around 3.9e-05, while ewald-rtol is 1.0e-05.
Generating 1-4 interactions: fudge = 0.5
WARNING 2 [file posre_Protein_chain_A.itp, line 233]:
Some parameters for bonded interaction involving perturbed atoms are
specified explicitly in state A, but not B - copying A to B
NOTE 2 [file newtop.top, line 25]:
The bond in molecule-type Protein_chain_X between atoms 18 CB and 31 DCG2
has an estimated oscillational period of 1.9e-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 is 6647.00
Number of degrees of freedom in T-Coupling group non-Protein is 126471.00
NOTE 3 [file ~/dssb_mdp/eqA/nvt-A.mdp]:
Removing center of mass motion in the presence of position restraints
might cause artifacts. When you are using position restraints to
equilibrate a macro-molecule, the artifacts are usually negligible.
There were 3 notes
There were 2 warnings
I think Warning_1 and Note_1 can be ignored as described by the book. But how about the Warning_2 and (especially) Note_2?
- Warning_2, posre_Protein_chain_A.itp, line 233:
453 1 1000 1000 1000
- Note 2: I think DCG2 atom for M2I exists in ‘develop’ branch and not in ‘master’ but why I still get oscillational period messages?
And also I have a question about the soft-core function. Most of the existing examples are using the sc parameters for sc-function=beutler. As now the GROMACS 2022 version supports sc-function=gapsys. Is it better to use this function instead?