Re: [AMBER] Assigning new velocities from Maxwell-Boltzmann distribution (ntx = 1)

From: Bill Ross <>
Date: Sun, 9 Aug 2020 23:27:45 -0700

It might be easier to begin equilibration if you assign velocities from
the forces on the atoms, or in any case either warm gradually or relax
restraints gradually.


On 8/9/20 1:43 PM, German P. Barletta wrote:
> Dear Amber users,
> I'm trying to enhance sampling by taking frames of interest from a run
> and assigning them new velocities to start new replica runs (poor man's
> adaptive sampling).
> When I start new replicas, I give them 5ns for "re-equilbration". The
> input for this re-equilibration is the same as the one for production but
> instead of reading velocities from the input file (ntx = 5), I assign new
> velocities at random (ntx = 1).
> The problem is, for some reason, Amber says the starting temperature
> (~450K) is way higher than it is supposed to be (temp0 = tempi = 300.0) .
> 100ps after, it's back to normal.
> Should I be worried? This happens with every replica I run. I'm attaching
> an output files from one of the replicas.
> I'd be thankful for any help.
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Received on Sun Aug 09 2020 - 23:30:02 PDT
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