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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 04 2020 - 09:30:01 PDT
