Hi,

Below is my .mdp code for pulling as found in the tutorial by Justin Lemkul. I made the required changes to match my version syntax.

pull = umbrella

pull_ngroups = 2

pull_group0 = Protein_chain_A

pull_group1 = DNA_chain_B

pull_group2 = DNA_chain_C

pull_geometry = distance ; simple distance increase

pull_dim = Y N N

pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns

pull_rate2 = 0.01

pull_k1 = 1000 ; kJ mol^-1 nm^-2

pull_k2 = 1000

pull_start = yes ; define initial COM distance > 0

When I tried to grompp using this code, it generates an error:

Fatal error:

Group topol_Protein_chain_A referenced in the .mdp file was not found in the index file.

Group names must match either [moleculetype] names or custom index group

names, in which case you must supply an index file to the '-n' option

of grompp.

I searched for the solutions in the Gromacs forum and found it might be due to name mismatch. But, in my case, the names are exactly same as referenced in the *.mdp file. Below is the molecule names from the topol.top file.

[ molecules ]

; Compound #mols

Protein_chain_A 1

DNA_chain_B 1

DNA_chain_C 1

SOL 33542

NA 125

CL 98

Can you please help to solve the problem? I tried with changing the names to Protein and DNA (the residue types) and changing the ngroups to 3. Nothing worked.

Update: I tried the code after making an index file. Grompp ran fine. But, after simulation it didn't produce any kind of "pull" i.e. shifting away of the DNA molecule from the protein.