Re: [AMBER] Generation of velocities depends on conformation?

From: Nicolas Cheron <>
Date: Thu, 8 Nov 2018 09:54:59 +0100

Dear Thomas, dear David,

Thank you for your clear answers. Now I understand more what's going on.


PS : David, yes I was using SHAKE

Le mer. 7 nov. 2018 à 13:52, David A Case <> a écrit :

> On Wed, Nov 07, 2018, Nicolas Cheron wrote:
> >
> > I plotted the temperature after the first step of MD and observed
> something
> > that puzzles me: the initial temperature is configuration dependent. By
> > that I mean that for a given conformation, all 200 temperatures are
> around
> > 400K. For another, the temperatures are around 350K. For others, around
> > 300K. After 1ps of simulation, all temperatures are randomly distributed
> > around 300K.
> To add to what Tom wrote: if you plot temperature vs. time, you will
> see that it takes far less than 1 ps for the temperatures to come into
> line with the thermostat. Are you using SHAKE? If so, what I suspect
> is happening is this: the algorithm in sander and pmemd to set initial
> velocities according to a Maxwell-Boltzmann distribution doesn't know
> about SHAKE, so you will get a spike in the temperature at the very
> beginning; as Tom pointed out, this goes away very quickly.
> If you are concerned about this, you can use the "setvelocity" action in
> cpptraj to make the proper corrections. [Developers: why don't we port
> this ability into sander and pmemd?]
> [Ignore the above if you are not using SHAKE.]
> ....dac
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Received on Thu Nov 08 2018 - 01:00:02 PST
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