GROMACS version:2018.1

GROMACS modification: No

I need to pull a drug situated in the hydrated region above the bilayer towards the center of mass (COM) of the bilayer using the umbrella sampling technique. For this process, I need to find the COM of the bilayer.

Kindly help me out in locating the COM of the bilayer such that I can estimate the distance and choose the reaction coordinate for the pulling.

Hi,

you can calculate the com of any group in your simulation system with **gmx traj -com**. For more information see **gmx traj -h**. The distance between the com of your drug and the com of the bilayer can be obtained via the selection algebra of **gmx distance**. For example:

**gmx distance -select ‘com of group “Drug” plus com of group “Membrane”’ -n drug.ndx** (I omitted the other flags of the command, look at gmx distance -h for more information).

The command assumes that “drug.ndx” contains an index group with the drug and all the lipids in your membrane. You can validate the distance calculation by using a molecular viewer (e.g. Pymol).

Cheers,

Marius

Hello Marius

I implemented your suggestion and used the command gmx traj to find the COM of the bilayer. But I could find an output from which I could not decipher the exact COM. I am attaching the plot here for your reference. Kindly help me out in understanding the output obtained.

Thanking in advance

Samapika

This is my command:

gmx traj -f …/pull_f.xtc -s …/pull.tpr -com yes -n index.ndx -ox bilayer.xvg

But I could find the COM of the bilayer from the bilayer.xvg by column averaging each X Y and Z column using a simple awk script.

Please suggest whether this approach is correct.

Thanks

Samapika

Seems correct to me.

Thank you so much for the help.

Consider some of the points explained in: On the in silico application of the center-of-mass distance method.