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Info about virtual atoms in MARTINI3
- moon
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2 years 10 months ago - 2 years 10 months ago #8983
by moon
Info about virtual atoms in MARTINI3 was created by moon
Dear
I'm testing my simulation system which includes a dimeric membrane protein and a lipid bilayer using martini 3. I tried starting a first minimization step with GROMACS but I get this note from grompp
In moleculetype 'molecule_0' 10 atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom.
In my protein for each monomer, I have 10 TRP so my guess is that this note is associated with the virtual sites on them. I am wondering if this is the case and I can proceed with the next steps or should I look more into the topology of my proteins for possible issues.
Thanks a lot for your help
Best
I'm testing my simulation system which includes a dimeric membrane protein and a lipid bilayer using martini 3. I tried starting a first minimization step with GROMACS but I get this note from grompp
In moleculetype 'molecule_0' 10 atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom.
In my protein for each monomer, I have 10 TRP so my guess is that this note is associated with the virtual sites on them. I am wondering if this is the case and I can proceed with the next steps or should I look more into the topology of my proteins for possible issues.
Thanks a lot for your help
Best
Last edit: 2 years 10 months ago by moon.
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- riccardo
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2 years 10 months ago #8984
by riccardo
Replied by riccardo on topic Info about virtual atoms in MARTINI3
I don't think this has to do with the virtual sites. I don't get any notes from grompp if using virtual sites for a molecule. I've just double-checked now with gromacs version 2019.5 and 2020. I think the problem lies elsewhere. Maybe try "Run with -v to get information for each atom." to get some more insights.
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- moon
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2 years 10 months ago - 2 years 10 months ago #8985
by moon
Replied by moon on topic Info about virtual atoms in MARTINI3
Thanks for the answer. If I use -v, GROMACS stops to give the notes about the atoms in the moleculetype of my protein. Also, the notes seem linked to TRP since if I create fake bonds for the TRP SC3 in my itp I do not get any more notes. But as you suggested the issue should be elsewhere, I will try to investigate.
Last edit: 2 years 10 months ago by moon.
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