Thank you Sir
On Mon, 6 Sep 2021, 8:40 pm Dr. Anselm Horn, <anselm.horn.fau.de> wrote:
> Dear Diganta,
>
> thanks for the update and pointing to that input variable.
>
> The Amber21 manual lists and explains on p. 363 only two options for
> ntx, either 1 or 5.
> This first option may be used for the initial MD, the second for a restart.
>
> (In the earlier Amber12 manual, options 1-6 but not 7 are given.)
> I assume, since the standard for coordinate/velocity input and Amber's
> abilities to autodetect the type of input (ASCII/binary) changed over
> time, the ntx=7 option is probably outdated, although it still occurs on
> p. 397 in the Amber21 manual.
>
> But the Amber experts may want to chime in here.
>
> Regards,
>
> Anselm
>
>
>
>
> On 09/06/2021 03:45 PM, Henry Green wrote:
> > Update on the Restart Problem : it has been observed that using NTX = 5
> > instead of 7 (for irest > 0) - intended to instruct the engine to read
> > coordinates and velocity data from the last .ncrst file seems to return
> the
> > temperature normally without any drop ( i.e. Temperature continues to
> > fluctuate about 300 K without dropping). In this regard I have come to
> know
> > from my Senior that the use of restraints did not change the temperature
> > drop; however using ntx = 5 has solved the problem on their system as
> well.
> > Apart from that, I was also told that this problem did not occur with the
> > PMEMD module of AMBER 18 (i.e. ntx = 7 did not cause the temperature
> drop)
> > and it seems the problem is being encountered only with ntx = 7 on the
> > SANDER module of AMBER 18. I am attaching some of the files that I was
> > shown by my Senior concerning this. Guidance regarding this is greatly
> > appreciated.
> >
> > Thanking you,
> > Diganta
> >
> > On Mon, 6 Sept 2021 at 11:05, Henry Green <henrygreen47k.gmail.com>
> wrote:
> >
> >> Respected Sir/Madam,
> >>
> >> My name is Diganta Dasgupta and I am a student in JNU, India. I have
> >> recently started to learn MD using AMBER. I am writing this mail to
> inform
> >> you of an error which I have encountered while doing so.
> >> I have started using AMBER 18 and was trying out the Tutorials
> >> provided at the AMBER website. In the Section 5 of Tutorial no. (5.2)
> >> titled "Simulating a DNA polyA-polyT Decamer" provided by Ross Walker
> Sir,
> >> which involves simulating the Decamer system in explicit solvent, it was
> >> mentioned that one should heat the system (to 300 K), after minimization
> >> (2-step), over a run of 20 ps in the NVT ensemble (using SHAKE on the
> >> Hydrogens and a weak restraint on the DNA), followed by a moderately
> long
> >> MD run in the NPT for Equilibration ( at 300 K). The .ncrst from
> >> minimization (only the coordinates) was to be used as the restart file
> for
> >> the heating step and the .ncrst from the heating (coordinates and
> >> velocities) was to be used as the restart for the Equilibration. Upon
> >> running the job as instructed and plotting the summary files on
> GNUplot, it
> >> was observed that initially the temperature rose as expected to 300 K
> >> within the 20 ps of heating simulation. However at the point of restart
> >> (i.e. right after the 20 ps mark) there is a sharp drop in Temperature
> by
> >> approx. 100 K and thereafter it again rose back to 300 K and stayed
> there
> >> the rest of the way.
> >> To further investigate this issue I ran the heating and
> Equilibration
> >> steps several times over with different break and restarts points and
> made
> >> the following observations :
> >>
> >> (i) The ensemble (NPT or NVT) did not matter and at each restart (
> >> irrespective of how many ps apart the restarts were done) there was a
> >> decrease in the temperature. I have tried breaking the 20 ps heating
> step
> >> into 2-3 steps and even in this I have observed the decrease at the
> restart
> >> points.
> >>
> >> (ii) The effect of this Temperature fall was observed in the other data
> >> like the Energy (Total, Potential and Kinetic - instead of reaching
> >> equilibrium values and fluctuating around the equilibrium values,these
> too
> >> decrease at the restart points),Pressure and Density.
> >>
> >> (iii) The .out file of the previous run shows final Temperature = 300 K
> >> and some energy values; however the next run's .out starts with
> different
> >> restart Temperature and energy values. This is observed at each break.
> >>
> >> From my Professor and Seniors I have come to know this issue was
> >> previously encountered on AMBER 18 but was not observed on running the
> same
> >> on AMBER 14.
> >> I understand that the Tutorial was made for the previous versions of
> AMBER
> >> and am confused regarding the cause of this error. Any guidance
> regarding
> >> this is much appreciated.
> >> I have herein attached the files for my last attempt at the
> simulation
> >> (this involves only the heating step; I have broken the heating step
> into 3
> >> parts : 1st is a 10 ps run with a 10 kcal/mol.A restraint on the DNA,
> 2nd a
> >> 6 ps run with a 5 kcal/mol.A restraint on DNA and the 3rd is a 4 ps run
> >> with 3 kcal/mol.A on the DNA.
> >>
> >> Thanking you,
> >> Diganta Dasgupta
> >>
> >>
> >>
> >>
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> >> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Mon Sep 06 2021 - 20:30:03 PDT
