Hi Erdem,
This happens when amber can't properly read the files of the previous
calculation.
If you used the same parameters in the tutorial, you need to change ntx=7
to ntx=5.
Best,
On Thu, Jun 4, 2020 at 7:07 PM David Cerutti <dscerutti.gmail.com> wrote:
> Yes, we'd need to see the mdin, but also the command you use to run this
> simulation on the command line. From the looks of it, I'd be you are
> unwittingly feeding the program the same input coordinates / restart file
> each time. It's also possible that you have something in the mdin that
> says to use a particular initial temperature and then reach a different
> temperature on average. However, 500 steps is a very small amount of
> dynamics for a thermostat to work over, so I'd suspect that you are seeing
> some other effect.
>
> Dave
>
>
> On Thu, Jun 4, 2020 at 11:58 AM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > 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 <erdemyeler.gmail.com>
> wrote:
> >
> > > Hello,
> > > I am trying to perform molecular dynamics simulation for DNA-ligand
> > > complex.
> > > For this, I used this tutorials and files
> > > https://ambermd.org/tutorials/basic/tutorial1/section5.htm
> > > 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: https://ibb.co/TRkzVxh)
> > > [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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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
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> >
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Büşra
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Received on Thu Jun 04 2020 - 14:30:02 PDT
