GROMACS version: 2019.1
GROMACS modification: No
Dear all,
I want to run MD simulation for a protein in membrane, with a single residue frozen completely. For membrane simulations, I have to use semiisotropic NPT ensemble. However, NPT does not work with frozen groups. I have found that previously energy group exclusions could be applied, which are now not supported. How can this issue be solved?
Thank you in advance,
Dmitrii
You will need to use a version that supports the group scheme (which I thought 2019 did, but if not, roll back to 2018) or otherwise simply use very strong position restraints. Freezing is entirely unphysical, anyway.
For modeling rock surfaces (e.g., carbonate reservoirs surface: modeled as calcite, CaCO3), since the surface atoms don’t move much, isn’t it better to freeze them? The location of those atoms will not change; that is what is needed for the rock surface.
Further, I observed that Gromacs always shift the system origin to 0 (the positions of all atoms will start from 0, i.e., in VMD, you will only see the right wall fluctuating, keeping the left wall frozen) when NPT is applied. So, when I have a system without any frozen atoms since all atoms can move, shifting the origin to zero is correct. However, when atoms are frozen, Gromacs will shift all atoms, excluding frozen atoms, which is wrong. If the default shifting to origin is removed, Gromacs can also be used for NPT of frozen atoms without applying position restraint. Awaiting your reply, @jalemkul.