GROMACS version: 2021.3 GROMACS modification: Yes/No Hi. I want to run a production step for a protein containing CU(II). How can I do this? What is the best user guide for me in this case? 1 post - 1 participant Read full topic

Dear gromacs users, I am working on a martini cg model of a mixed bilayer system. However I am a bit confused about choosing the correct box length using editconf. If I use gmx editconf -c -d 1.0 i.e. keeping 1 nm distance between the bilayer and the box, then the resulting box size is very large. Generally for proteins we follow this protocol of choosing a box length where the pro…

Dear gromacs users, This is more of a general question I have regarding removal of PBC effects from simulation trajectory. I have seen that some of the online tutorials mention the removal of PBC for analysis and some of the tutorials use raw production MD trajectory for further analysis without correcting the trajectory for PBC. Some of the tools such as: gmx rms, rmsf, distance …

GROMACS version: 2021.5 GROMACS modification: No Hello I’m trying to simulate a system with 8 identical peptides and a lipidic membrane, but I want the peptides to interact with only one leaftlet of the membrane. I was told to use Flat-Bottomed position restraints to keep the peptides on one side. But it’s not working as intended, I’ve run a test for 200 ns and the peptides appea…