Question about CHARMM-GUI NAMD Inputs

From: Ahmad Alqaisi (
Date: Sun Dec 26 2021 - 18:41:30 CST

Hello all,

I have been using the CHARMM-GUI server to generate NAMD input files for MD
simulations. I noticed that inputs from this server give bad results in
many cases, especially in terms of RMSD values and simulation stability.

Can you give any suggestion on how to improve the inputs generated by
CHARMM-GUI to get better results? For example, the equilibration time in
the CHARMM-GUi protocol is much smaller than other protocols like QwikMD.
If I increase the equilibration time, would that give me better results?

Also, can anyone give a description of the protocol that is carried in the
CHARMM-GUI input files ? For example the file named
step4_equilibration.inp, does it contain minimization, annealing and
equilibration or only minimization and equilibration?

Ahmad Alqaisi

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