GROMACS version:2021.1
GROMACS modification: no
Hi all,
I am Subhasree, want to start MD simulation on protein cold denaturation. From previous studies I got to know that people are using TIP4P/2005 water model for very cold temperature as it’s optimised for that. As it’s not inbuilt in Charmm36-jul2021 so I need the .itp file and .gro file for using this water model. But I am unable to find the .gro file. I got the .itp file from one website. Please help me to get the .gro file. And give me suggestions regarding this issue.
Thanks and regards,
Subharee
If you look here and here, you can see that the only difference between TIP4P and TIP4P/2005 in terms of geometry is the location of the virtual site. You could copy the .gro file for TIP4P and edit it such that r_OM (the oxygen-virtual site distance) is the correct value.
thank you so much for your suggestion. I will try the same