Dear Busra, thanks for your answer. I will try your suggestion.
Dear Carlos and David here is my mdinfo file:
NSTEP = 50000 TIME(PS) = 22100.000 TEMP(K) = 299.66 PRESS =
-120.4
Etot = -61371.8828 EKtot = 13056.1609 EPtot =
-74428.0437
BOND = 209.1219 ANGLE = 486.6141 DIHED =
728.9482
1-4 NB = 219.3220 1-4 EEL = -3907.1373 VDWAALS =
9379.6505
EELEC = -81544.5632 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 6296.8241 VIRIAL = 6863.7512 VOLUME =
218013.7641
Density =
1.0152
Ewald error estimate: 0.1911E-03
| Final Performance Info:
| -----------------------------------------------------
| Average timings for last 100 steps:
| Elapsed(s) = 5.16 Per Step(ms) = 51.57
| ns/day = 3.69 seconds/ns = 23442.84
|
| Average timings for all steps:
| Elapsed(s) = 2584.57 Per Step(ms) = 51.69
| ns/day = 3.68 seconds/ns = 23496.11
| -----------------------------------------------------
Busra Demir <bdemir09.gmail.com>, 5 Haz 2020 Cum, 00:20 tarihinde şunu
yazdı:
> 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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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Büşra
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Received on Sat Jun 06 2020 - 16:00:02 PDT
