On Fri, Oct 02, 2015, Kalenkiewicz, Andrew (NIH/NICHD) [F] wrote:
>
> I am trying to start an accelerated MD simulation from an equilibrated
> system using a random seed (ig=-1) for the velocities, but for some
> reason there is a large temperature spike at the beginning of my
> simulation when I use the following input file:
>
>
> The temperature starts at ~430K, drops to around 270K, and then
> equilibrates to 300K. But according to the manual:
I suspect that the velocity randomization procedure doesn't properly recognize
the fact that bonds to hydrogen are being shaken. Try a short test simulation
without shake to see if you get good initial temperatures.
cc-ing to the Amber developers' list, since this is arguably something that
ought to be fixed. I think(?) there is code in libsff that addresses this,
but that doesn't help much for pmemd users. (Also worth checking mdgx....)
Volunteers are welcome...this is how you get established in a community.
My start in Amber was to volunteer to add second derivative code. I
polished up that code so faithfully, that now I am the ruler of the
Queen's Navy....
....dac
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Received on Sun Oct 04 2015 - 23:30:03 PDT
