[gmx-users] calculating work done in SMD using gromacs 5.1.2

Chinmai P chinmai.p at gmail.com
Wed May 9 16:58:24 CEST 2018

Hi all,
I have performed steered MD simulations for pulling ligand through the
tunnel of protein. This is done in three parts where in the first part
ligand is pulled towards the centre of tunnel using COM of residues in the
centre as reference, in second part the ligand is pulled further from
centre to the tip of tunnel by using COM of residues at tip.In the third
part, in order to bring the ligand completely out from protein, it was
pushed out from tip to the exterior of protein Since. the entire trajectory
is divided into 3 parts with different references, I am confused how to
calculate the total work done for pulling ligand from one end of tunnel to
Kindly help.

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