Its not clear what you want. I guess you are looking for the selection of few water molecules to apply the foce. If so, you can use gmx make_ndx and create index file to use for pulling simulation.

Hi Nikhil,

Thank you for your suggestion!

I do need to create an index of water molecules to apply the force, and I have tried gmx make_ndx, and it only generates a fixed index of water molecules depending only on the initial positions of the molecules.

But in my case, the list of selected water molecules is dynamic, it changes with the simulation. I want to tell Gromacs to apply the force only on the water within the specified area. The area is always fixed, the molecules within it are changing with the silumation. And so the water molecules in the list should be updated during the simulation for every 10 ps.

So could you please give me some more suggestion.

Thank you.

Best regards,

Qingran

Nikhil Maroli

Hi Wojciech,

Thank you for your suggestion!

I will try the modified version of Gromacs.

Thanks again!

Best regards,

Qingran

Wojciech Kopec

Hi Wojciech,

I have tried the modified version of Gromacs (sliced pull), however, when I use the gmx grompp, it says as below and the PC seems to be working for really a long time

-----------------------------------------------------------------------------------------------

...

Number of degrees of freedom in T-Coupling group Water_and_ions is 6771.28

Number of degrees of freedom in T-Coupling group MOL is 689.72

Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K

Calculated rlist for 1x1 atom pair-list as 1.011 nm, buffer size 0.011 nm

Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm

Note that mdrun will redetermine rlist based on the actual pair-list setup

Calculating fourier grid dimensions for X Y Z

Using a fourier grid of 40x16x16, spacing 0.150 0.160 0.154

-----------------------------------------------------------------------------------------------

Could you please give me some advice on

What does this step mean and can I skip this step in order to make a quick grompp?

The code files are attached below.

Thank you very much!

Best regards,

Qingran

Wojciech Kopec