Re: [AMBER] duplicate simulations problem

From: Sadaf Rani <>
Date: Thu, 25 Nov 2021 00:08:38 +0500

Dear Dr. David
Thank you very much for your kind reply. I am running these simulations on
GPU. yes, I am using the same combination as you mentioned .e.g. ntt=3 and
ig=-1. Does it mean that although the simulation has varying results the
convergence should be similar? Could you please give your comments on
it how should I proceed with the duplicate run of simulation? Either I need
to give the same seed number?

I am using the following input file for Equilibrations and production runs:-

Heating up the system equilibration stage 1 50ps
  imin=0, nstlim=100000, dt=0.0005, ntx=1, irest=0, ntpr=5000, ntwr=5000,
  tempi =0.0, temp0=50.0, ntt=3, tautp=2.0, ig=-1 gamma_ln=1,iwrap = 1,
  ntb=1, ntp=0, ntr=1,
  ntc=2, ntf=2,

Constant pressure constant temperature equilibration stage 1
  imin=0, nstlim=100000, dt=0.0005, ntx=5, irest=1, ntpr=5000, ntwr=5000,
  temp0=300.0, ntt=3, taup=2.0, gamma_ln=5,

  ntb=2, ntp=1, pres0 = 1.0,

  ntc=2, ntf=2,ntr=1,


Constant pressure constant temperature production run
  nstlim= 10000000, imin=0, dt=0.002, ntx=5, irest=1, ntpr=5000, ntwr=5000,
  temp0=300.0, ntt=3, tautp=2.0, gamma_ln=5.0,

  ntb=2, ntp=1,

  ntc=2, ntf=2,

Looking forward for your suggestions.
Thanks in advance.

On Wed, 24 Nov 2021 at 18:35, David A Case <> wrote:

> On Wed, Nov 24, 2021, Sadaf Rani wrote:
> >I run a simulation of a protein-ligand complex. To verify its results I
> >rerun the same simulation under the same conditions but I got
> >different results. e.g. RMSF and bond distances of some key residues under
> >investigation are different.
> >I am unable to identify the reason for this difference although the inputs
> >are the same.
> Without having more information (such as your mdin file), I have to make
> guesses.
> One common situation is to use ntt=3 and the default value of ig (which is
> -1). This combination will use a different random number generator for
> each
> run, leading (by design) to different results. It is generally recommended
> that you indeed run repeated simulations in this manner, as a simple check
> on reproducibility and convergence.
> A second (perhaps less common) situation arises if you have irest=0 and
> tempi > 0.
> Third possibility: you are running parallel simulations on a CPU.
> If none of these apply to you, we will need more information.
> ....dac
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Received on Wed Nov 24 2021 - 11:30:02 PST
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