GROMACS modification: Yes/No
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Hi. I am a little bit confused with energygrps and energygrp-excl. In the given example of gromacs:
energygrp-excl = Protein Protein SOL SOL
Does it mean that the molecules of protein will not interact with the molecules of solvent? What about the interactions of protein molecules with other protein molecules? Why are duplicate names used (SOL SOL)? If I want in a simulation to turn off the non-bonded interactions between same species is that possible?
Thank you in advance!
Imagine that you have the following groups in your system Protein_A, Protein_B and SOL. Note the group name refer to name given in index file.
“energygrp-excl = Protein_A Protein_A SOL SOL” means that all non-bonded interactions between Protein_A and Protein_A are excluded and that all the non-bonded interactions between SOL and SOL are excluded.
Does it mean that the molecules of protein will not interact with the molecules of solvent?
No, only the non-bonded interactions between the protein and the solvent are included.
Why are duplicate names used (SOL SOL)?
The energy group exclusion is always given in pair that is the reason
I hope it is more clear.
Thank you a lot for your answer. Just a clarification. I want to exclude non-bonded interactions between same species that are not classified as proteins. Specifically, I am working with polymers, so I made a .ndx file and included all the atoms in a [ IPP ] group. Then, in the .mdp file, I used the options:
energygrps = IPP
energygrp-excl = IPP IPP
Is that correct?
The name corresponds to molecule names defined at the end of your topology file. If your polymer is defined IPP at the end section of topol.top that it is good.
One is not limited to
[moleculetype] entries for
energygrps. Any index group should work fine.
Note that energy group exclusions are no longer supported since version 2020, because they were only supported with the group scheme. We intend to support these again at some point in time. If the molecules you want to exclude interactions between only contain atomtypes that do not occur in the rest of the system, you can achieve the same by setting the LJ pair parameters between these atomtypes to 0.
Thank you. I have already read this in the manual. But I am using an older version for this purpose. Indeed, It is a useful option to have it.
Is this done in [ pairtypes ] in the forcefield.itp file, where you have to list all the permutation of atoms between the two groups of molecules and write zeros for sigma and epsilon?
No, the non-bonded pair parameters are in the [ nonbond_params ] section.