Partial tempering changes charge of protein?

[Blue Schmitz]

Hey everyone, 

I am trying to set up HREX MD simulations following this tutorial: https://www.plumed-tutorials.org/lessons/22/010/data/INSTRUCTIONS.html

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:

NOTE 2 [file scaled_0.5_all.top, line 52019]:
  System has non-zero total charge: 0.020571
  Total charge should normally be an integer. See
  https://manual.gromacs.org/current/user-guide/floating-point.html
  for discussion on how close it should be to an integer.

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

[Giovanni Bussi]

Hello.

Can you share your top and gro file?

Giovanni

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[Raine Filex]

hello  Giovanni,

I encountered similar problems, and the LJ energy is not “half” compared to the non-scaled simulation.

********************************************************************************************************************************

Command line:
  gmx_mpi grompp -f md.mdp -o sc0.5.tpr -c eq.gro -p scaled0.5.top -n index.ndx
NOTE 1 [file scaled0.5.top, line 1427193]:
  System has non-zero total charge: 0.292893

********************************************************************************************************************************

Attached are my gro and top files.

[Giovanni Bussi]

You have a molecule with charge -1, in a solution with 739 Na+ and 738 Cl-.

You scale the charges of the molecule by a factor sqrt(1/2), which results in a molecule with charge -0.707. You did not scale the ions instead. The total charge is -0.707+1=0.293, as expected.

I don't see any problem

Giovanni

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