Re: [AMBER] Equilibration in multiple steps with decrement in force constants

From: Carlos Simmerling <>
Date: Mon, 1 Apr 2019 07:11:30 -0400

Yes equilibration is typically done in multiple steps with decreasing force
constants. However this doesn't use k1 etc. Maybe you can post your input
and the section of the output that gives the first energies so we can see
what you did and what happened.

On Mon, Apr 1, 2019, 6:20 AM Priyabrata Das <> wrote:

> Dear all,
> I am a beginner in Amber and wanted to know if the equilibration step can
> be done in multiple steps with decreasing the force constant.
> I am working on DNA molecular dynamics simulation. Prior to equilibration,
> I have done minimization and heating(from 0 to 300k with K=20 for 20ps).
> When equilibrating the system with decreasing force constant (K1=20, K2=10,
> K3=5, K4=1, and without constraints). During the starting of the second
> step of equilibration (K2=10) temperature is shooting up to 700 K. After
> that everything is going well. Should I continue or this can cause any
> problem?
> Thanks
> Priyabrata Das
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Received on Mon Apr 01 2019 - 04:30:02 PDT
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