Comments (4)
Potentially you should be able to resolvate a system that was previously solvated and specify a new ion concentration. This would keep all existing water molecules, then adjust the ion concentration accordingly. (This isn't something that I've tested.)
Alternatively, you could replace some of the water molecules in the system with ions. This is not super easy given the current API but I could try to come up with an example script if the above doesn't work. (You could always just edit the top file that is generated if you know what you are doing.)
from biosimspace.
Thanks, @lohedges. My issue, as you describe in option 1, for a membrane system, water molecules are inserted in the membrane. Is there any way to avoid it?
from biosimspace.
Ah, I see. We currently don't provide support for membrane simulations. This is a know issue with gmx solvate
(our solvation backend) and they describe the issue, and some suggested workarounds here. We don't support the radius
option that they suggest, but could look into it if useful. Previously we've found that some of the options don't always behave as you would logically expect, so have limited using them and let people use gmx solvate
manually if desired.
from biosimspace.
Thank you for this explaination. I am dealing with a situation wherein the water in the topology file is not continuous, for example:
Protein 1
Water 4
Ligand 1
Water 100
In order to put ions in this system with gromacs command, genion, I need to edit gro/pdb and topology file so that the water molecules enties are continuous. With BioSimSpace, I am able to solvate and Ionize these kind of systems , and was wondering do you take care of this ineranlly so that you are able to put ions in this system? and If yes, is it possible to get access to these objects or write them out as gro/pdb and top file?
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Related Issues (20)
- Storage quota exceeded on the Anaconda cloud HOT 1
- HILLS file not updating during restarting simulation HOT 4
- Problem when converting Gro/Top to Rst7 HOT 12
- Making HMR work with dummies HOT 11
- Make _removeDummies() recognise dummy bonds HOT 10
- Would it be possible to include HiMap as an alternative to LoMap in the generateNetwork method? HOT 2
- Unable to import BioSimSpace after mamba installation HOT 12
- BioSimSpace.Align.viewMapping: py3Dmol.view not rendering in Jupyter Notebook HOT 11
- `_toRegularMolecule` failing with `convert_amber_dummies=True` HOT 15
- Absolute Binding Free Energy Calculations with GROMACS HOT 7
- Pickling a parametrised molecule from an SDF file with GAFF2 HOT 4
- Are atomtypes meant to be updated when using repartitionHydrogenMass? HOT 16
- [BUG] OSError "It looks like you failed to include a topology file." when reading SDF which doesn't contain redundant bond order information HOT 10
- [BUG] Cannot import BioSimSpace after installation of biosimspace 2023.1.2 using mamba HOT 3
- AnalysisError: SOMD free-energy analysis failed! HOT 5
- [BUG] HOT 10
- Reporting a vulnerability
- [BUG] Water molecule coordinates are setting to (0,0,0) HOT 4
- Issue in reproducing the funnel methadynamics tutorial HOT 2
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from biosimspace.