Re: [GaMD-discuss] GaMD Equilibration Time Query

[Miao, Y. <Yin...@me...>]

Hi Christine,

It seems ok to shorten your equilibration simulation.

Meanwhile, you may set a larger number for “accelMDGStatWindow”, which could be roughly 4 times the total number of atoms in your system.

Best,
Yinglong

Yinglong Miao, Ph.D.
Associate Professor
Department of Pharmacology and
Computational Medicine Program
University of North Carolina - Chapel Hill
Tel: 1-919-962-5696
http://miaolab.org

Editor-in-Chief
npj Drug Discovery
https://www.nature.com/npjdrugdiscov

On Jun 20, 2025, at 1:52 PM, Christine Qian <chr...@uc...> wrote:

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Dear GaMD developers,

I am running GaMD on several protein (a monomer of 42 residues)-membrane systems with waters and ions. The systems have sizes of about 170000 atoms. This is the parameters that I'm using for my equilibration:
# GaMD Equilibration Params _________________________
accelMD                                         on
accelMDdual                                     on
accelMDdihe                                     on
accelMDG                                        on
accelMDGiE        1
accelMDGRestart  off

accelMDGcMDPrepSteps    200000
accelMDGEquiPrepSteps   200000
accelMDGStatWindow      20000

accelMDGcMDSteps        1000000
accelMDGEquiSteps       25000000
accelMDOutFreq          1000

accelMDGsigma0P 6.0
accelMDGsigma0D 6.0

run 26000000
I've noticed from the log file for all of my systems that the k0d and k0p values reach 1 really early (at about step 1210000) and then stay at 1 throughout. However, I'm afraid that it's a bit too fast. Is this behavior normal? Do my parameters look ok?

If everything looks alright, is it ok that I shorten the equilibration time a bit, or should I keep it at 50 ns?

Thank you so much for your help!

All the best,
Christine Qian


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