Hey everyone,
Under exercise 2a, it says to add underscores to all atoms (in the type column) that I want to scale, like this:
1 HC 1 ACE HH31 1 0.1123 1.008 ; qtot 0.1123
1 HC_ 1 ACE HH31 1 0.1123 1.008 ; qtot 0.1123
Now for the second sanity check in exercise 2b, one must scale all atoms with a factor of 0.5 (including the solvent), to see whether the energies are correctly multiplied by 0.5, meaning whether the scaling worked. So I have added _ after every atom type in the [ atoms ] section, and additionally to the water:
[ atoms ]
; id at type res nr res name at name cg nr charge mass
1 OW_ 1 SOL OW 1 -0.834 16.00000
2 HW_ 1 SOL HW1 1 0.417 1.00800
3 HW_ 1 SOL HW2 1 0.417 1.00800
and ions:
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 Cl_ 1 CL CL 1 -1.00000
However, when I now run gmx_mpi grompp -f ./sanity_check.mdp -c ../npt_5.gro -p ./scaled_0.5_all.top -o scaled_0.5_all.tpr, I get the note and warning:
WARNING 2 [file scaled_0.5_all.top, line 52019]:
You are using Ewald electrostatics in a system with net charge. This can
lead to severe artifacts, such as ions moving into regions with low
dielectric, due to the uniform background charge. We suggest to
neutralize your system with counter ions, possibly in combination with a
physiological salt concentration.
I had neutralized the system before, and ran a short simulation where only a few atoms were scaled and not the solvent, so I believe the partial tempering is messing with the charge. Has anyone ever run into that problem? Do I need to add the _ to a different column for the water and ions? I have not found any documentation on that.
I appreciate every tipp!
Kind regards,
Blue