If you already have relaxed the system I would not reset the temperature to
a low value, especially with that thermostat (ntt=1).
Ntt=3 and ig=-1 will give different trajectories even if you read in the
velocities.
If the triplicates are not agreeing then it is a sign that the protocol is
not reproducible. Perhaps it needs to run longer, or have other
adjustments, but that depends on your project and the timescale of the
motions you are modeling. Maybe it is related to your aMD setup.
On Fri, Sep 8, 2023, 3:33 PM Romero, Maria via AMBER <amber.ambermd.org>
wrote:
> Hello Amber community,
>
> My goal is to generate triplicate aMD runs for my system, but I have been
> struggling to obtain results that agree with each other to a certain
> extent. These are the two methods that I have tried so far:
> -Starting with one single pdb structure, do prep in cpptraj and
> minimization and then introduce random velocities in my first step of
> equilibration using the following script:
>
> nstlim=250000, dt=0.001, ntx=1, irest=0, ntpr=1000, ntwr=10000, ntwx=1000,
> tempi=0.5, temp0=300.0, ntt=1, tautp=2.8, ig=-1,
> ntb=1, ntp=0,
> ntc=2, ntf=2,
> cut=10.0, iwrap=1
>
> The results from the 3 trajectories do not agree at all. For example my
> ligand would randomly leave one of the active sites in one trajectory, both
> active sites in another and none in the third trajectory.
>
> The second approach I tried was:
>
> -Take 3 different starting structures from an unbiased MD simulation as
> starting points and using the following script for the first step of
> equilibration:
>
> nstlim=250000, dt=0.001, ntx=1, irest=0, ntpr=1000, ntwr=10000, ntwx=1000,
> tempi=000.0, temp0=300.0, ntt=1, tautp=2.8, ig=-1,
> ntb=1, ntp=0,
> ntc=2, ntf=2,
> cut=10.0, iwrap=1,
>
> Which I guess introduces velocities based on the forces, but again results
> are very different.
>
> Can someone help? Should I use a different thermostat like ntt=3? My
> system is dimer protein solvated in water. What is the best way to
> introduce random velocities that would give me trajectories that are
> similar to each other? My big concern is reproducibiliity.
>
> Thank you in advance for your help,
> Maria.
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>
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Received on Fri Sep 08 2023 - 14:00:03 PDT
