How to Apply Flat-Bottom Potential to a Specific Chloride Ion During Umbrella Sampling

User discussions
1

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

2

Hi Prashant,

Yes, that’s possible, have a look at the mdp reference. Since you already specified an index group for the specific chloride ion you want to pull through the protein, you can specify this using the pull-group1-name option. You can also use a flat-bottom potential by setting pull-coord1-type to flat-bottom, but for performing umbrella sampling the option umbrella would be more appropriate.