- Posts: 13
Solvation with ref_PW model
- bond_007
-
Topic Author
- Offline
- Fresh Boarder
Less
More
4 years 6 months ago - 4 years 6 months ago #8279
by bond_007
Solvation with ref_PW model was created by bond_007
Hello,
I am trying to solvate a protein dimer using the ref-PW water model. The box size is ~ (24x24x24 nm).
The command is - gmx_mpi solvate -cs polarizable-water.gro -cp protein.gro -radius 0.21 -p topol.top -o solvated_protein.gro
However, after solvation when I check the density, it is around 300 g/L. So it seems like the number of water molecules added are two few. Therefore, during an NPT equilibration, the volume of the box is reduced drastically so that the density fluctuates around 1000 g/L.
But I don't want my box size to change to such an extent an want it to be around (~24 nm in x,y,z). I can think of two ways to accomplish this -
1) While solvation using gromacs, reduce the vdw radius so more molecules can fit in. This could increase the density and prevent a decrease in volume during equil. But this could also lead to problems during equil runs due to high forces.
2) Do some NPT equil runs and solvation runs one after the other, until I get the required box size with appropriate density.
Do you have any other suggestions to do this?
The density of the reference structure for ref_PW is around 1000 g/L, so I don't understand why I don't get a similar density (adding more molecules) when I solvate the protein.
I am trying to solvate a protein dimer using the ref-PW water model. The box size is ~ (24x24x24 nm).
The command is - gmx_mpi solvate -cs polarizable-water.gro -cp protein.gro -radius 0.21 -p topol.top -o solvated_protein.gro
However, after solvation when I check the density, it is around 300 g/L. So it seems like the number of water molecules added are two few. Therefore, during an NPT equilibration, the volume of the box is reduced drastically so that the density fluctuates around 1000 g/L.
But I don't want my box size to change to such an extent an want it to be around (~24 nm in x,y,z). I can think of two ways to accomplish this -
1) While solvation using gromacs, reduce the vdw radius so more molecules can fit in. This could increase the density and prevent a decrease in volume during equil. But this could also lead to problems during equil runs due to high forces.
2) Do some NPT equil runs and solvation runs one after the other, until I get the required box size with appropriate density.
Do you have any other suggestions to do this?
The density of the reference structure for ref_PW is around 1000 g/L, so I don't understand why I don't get a similar density (adding more molecules) when I solvate the protein.
Last edit: 4 years 6 months ago by bond_007.
Please Log in or Create an account to join the conversation.
- riccardo
-
- Offline
- Platinum Boarder
4 years 6 months ago #8282
by riccardo
Replied by riccardo on topic Solvation with ref_PW model
Either 1) or 2) could work indeed. Option 3), which is maybe what you mean with 2) but I'm not sure, it's to make a much larger box for the protein.gro so that it shrinks back to your desired 24x24x24 nm3. That'd require a few trails.
The "problem" is with the gmx solvate tool, but either 1) or 2)/3) should easily fix the issue.
The "problem" is with the gmx solvate tool, but either 1) or 2)/3) should easily fix the issue.
Please Log in or Create an account to join the conversation.
Time to create page: 0.087 seconds