Re: [AMBER] Restart

From: Dr. Anselm Horn <>
Date: Mon, 6 Sep 2021 17:10:00 +0200

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time, the ntx=7 option is probably outdated, although it still occurs on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.



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 <> 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 Mon Sep 06 2021 - 08:30:02 PDT
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