On Mon, 6 Sept 2021 at 11:28, Henry Green <henrygreen47k.gmail.com> wrote:
>
>
> 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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Received on Sun Sep 05 2021 - 23:30:02 PDT
