Re: [AMBER] What is happening in my Molecular Dynamics in the beginning of every 500 steps ?

From: Carlos Simmerling <>
Date: Thu, 4 Jun 2020 11:57:57 -0400

is this 1 continuous MD run you are showing? it might help to share the
mdin file

On Thu, Jun 4, 2020 at 11:35 AM Erdem Yeler <> wrote:

> Hello,
> I am trying to perform molecular dynamics simulation for DNA-ligand
> complex.
> For this, I used this tutorials and files
> all minimization, heating and production files are the same with this
> tutorial. But instead of tutorial's DNA I used 1BNA PDB code DNA and I u
> sed my ligand as well.
> After I docked my ligand and 1BNA, I made my DNA-ligand complex and then I
> used gaff and my novel force field frcmod file for the ligand after I
> solved my complex in TIP3P water I followed the instruction the tutorial I
> mentioned above.
> Result was very surprising here is my volume chart
> (if it does not seem chart is here:
> [image: image.png]
> and my kinetic and potential energy charts are similar. in the beginning
> of every 500 steps, volume and energy is dropping suddenly then everything
> going up normal. My computational power is not big so I couldn't try
> another method. My questions are
> 1) What is happening in the beginning of every 500 steps?
> 2) Is this normal or something went wrong?
> 3) if it is wrong how can I solve this?
> Thank you
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Received on Thu Jun 04 2020 - 09:00:03 PDT
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