Simulation of imprinting process in NAMD

From: Abhaysinh Gaikwad (ahgaikwa_at_aggies.ncat.edu)
Date: Tue Jan 30 2018 - 10:52:50 CST

Hello,

I am trying to simulate an imprinting process using NAMD. In an imprinting
process a solid stamp comes down on to the substrate to generate the its
profile on the substrate and then stamp is pulled back. I am using
following methods,

1) to keep the stamp geometry and shape intact throughout the process -
rmsd colvar (without rmsd colvar the structure does not maintain its shape)

2) to move stamp up and down - Steered Molecular Dynamics

3) to conduct the process and get the deformation in the substrate -
increasing the temperature of system slowly by reassigning velocities at
different steps.

I am looking for stresses developed in the substrate during and after the
process. Could you please suggest me how to get the stresses. Also, let me
know if I am going wrong somewhere.
I am using Lennard-Jones potential and CHARMM.

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