GROMACS version: 2018.8
GROMACS modification: No
Hello everyone,
I am performing an umbrella sampling simulation* in GROMACS where I’m pulling a chloride ion through the pore of a ** membrane protein** embedded in a lipid bilayer. My system is neutralized using KCl, so there are multiple chloride ions present.
However, I want to apply a flat-bottom potential only to the specific Cl⁻ ion that I am pulling (residue number 526). I do not want this potential applied to the other chloride ions in the system.
What would be the best way to implement this? I initially thought of editing the .itp file for chloride, but since that would affect all chloride ions, it doesn’t seem like the right approach.
Is there a way to define a flat-bottom harmonic potential using the pull code that applies only to this specific ion, perhaps using an index group? If so, how should I configure my pull.mdp file and index file to achieve this?
Any help or suggestions would be greatly appreciated! I have attached my .mdp file for pull
and my index file groups are as such :
0 System : 74658 atoms
1 Protein : 3595 atoms
2 Protein-H : 1801 atoms
3 C-alpha : 225 atoms
4 Backbone : 675 atoms
5 MainChain : 899 atoms
6 MainChain+Cb : 1113 atoms
7 MainChain+H : 1113 atoms
8 SideChain : 2482 atoms
9 SideChain-H : 902 atoms
10 Prot-Masses : 3595 atoms
11 non-Protein : 71063 atoms
12 Other : 71063 atoms
13 POPC : 30418 atoms
14 POT : 37 atoms
15 CLA : 42 atoms
16 TIP3 : 40566 atoms
17 chloride_pull : 1 atoms
18 chloride : 41 atoms
19 Protein_chloride_pull: 3596 atoms
20 POT_CLA_TIP3 : 40644 atoms
21 tm_c-alpha : 157 atoms
pull.mdp (2.6 KB)
Thank you,
Prashant