GROMACS version: 2025.2
GROMACS modification: No
I’m working on a pulling simulation in GROMACS where I want to apply a force between atom N01 of a GUA residue and atom O05 of an ACE group. I’m trying to pull them apart by 1 Å over 0.5 ns, so I’ve set the pull rate to 0.0002 (2 Å/ns). I’m a bit confused about how to correctly define the pull_group1_name and pull_group2_name should I define them based on the residues (GUA and ACE) or create custom index groups for just N01 and O05 ? I’m not sure how to handle this in the .ndx file or the .mdp settings. I’ve attached my .mdp and .gro files in case that helps clarify things. Your tutorials have been a huge help, and I’d really appreciate any advice you can give on setting this part up.
Thank you for all the support.
md_pull.mdp (2.4 KB)
My Gro file is as follows-
God Rules Over Mankind, Animals, Cosmos and Such
19
1GUA H00 1 0.168 0.169 -0.000
1GUA N01 2 0.163 0.068 0.000
1GUA C02 3 0.042 0.003 0.000
1GUA H03 4 0.251 0.017 0.000
1GUA N04 5 0.058 -0.134 0.000
1GUA N05 6 -0.069 0.070 0.000
1GUA H06 7 0.150 -0.176 0.000
1GUA H07 8 -0.022 -0.197 0.000
1GUA C08 9 -0.193 -0.007 -0.000
1GUA H09 10 -0.202 -0.069 0.089
1GUA H0A 11 -0.202 -0.069 -0.090
1GUA H0B 12 -0.278 0.062 0.000
1ACE H00 1 0.637 -0.222 -0.024
1ACE C01 2 0.565 -0.247 0.055
1ACE C02 3 0.430 -0.187 0.023
1ACE H03 4 0.560 -0.356 0.063
1ACE H04 5 0.603 -0.206 0.150
1ACE O05 6 0.430 -0.060 0.013
1ACE O06 7 0.336 -0.269 0.011
0.00000 0.00000 0.00000