GROMACS version: 2023
GROMACS modification: No
Here post your question
GROMACS Tutorial
Building Biphasic Systems
I have made this tutorial with biphasic system and the referenced files but i cannot do energy minimization as i dont have the topoloy for the whole system. What can i do?
Are you referring to the energy minimization of chx_box.gro? chx.top should work as the topology file, you just need to change the number of molecules at the bottom of the chx.top file under [ molecules ] to match the number you generated for chx_box.gro. For example, I used random insertion and got a box of 1039 CHX molecules, so that’s the number I used
There is a topology file provided in the tutorial and as Karis notes, you may just have to update the number of CHX molecules in it. Then if you add water as the tutorial shows you via gmx solvate, it will update the topology with the number of water molecules it added. The #include statement for the SPC topology is already in chx.top in preparation for this step.
Thank you for your replies! I will try them and update you!
Dear Sir, I have a follow up question related to this building a biphasic system GROMACS tutorial. So when doing NVT and NPT equilibration can I use the same chx.top file given in the tutorial. And am I supposed to delete “define = -DPOSRES” line in the nvt.mdp and npt.mdp files since I don’t have a posre.itp file given in the tutorial? please help me with this. Thank you.
Could you suggest a correct way to get index file for nvt.mdp? The problem is that the generated system appears as 3 different group with just one kind of residue. How is it possible to obtain 2 groups? Thanks!
You don’t need two groups if you’re referring to tc-grps. Just set tc-grps = system.
Thanks a lot! It worked.