[AMBER] Generation of velocities depends on conformation?

From: Nicolas Cheron <nicolas.cheron.boulot.gmail.com>
Date: Wed, 7 Nov 2018 11:44:11 +0100

Dear all,

I have 20 conformations of the same protein-ligand system (obtained via
previous sampling). For each of these conformations, I generated with Amber
new velocities 200 times and performed a short simulation (all input files
are the same (except the .rst file) and target temperature is 300K).

I plotted the temperature after the first step of MD and observed something
that puzzles me: the initial temperature is configuration dependent. By
that I mean that for a given conformation, all 200 temperatures are around
400K. For another, the temperatures are around 350K. For others, around
300K. After 1ps of simulation, all temperatures are randomly distributed
around 300K.

Is it a known behaviour? I am also surprised that while asking for a
temperature of 300K, the initial temperature is at 400K. Can someone please
explain me how the velocities are initially assigned to each atom?

Thank you for your help.

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Received on Wed Nov 07 2018 - 03:00:03 PST
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