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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Received on Sun Sep 05 2021 - 23:00:02 PDT
