Couldn't one overcome the problem that "nothing happens" by temperature
replica exchange?
Best,
Andy
Am 3/8/2018 um 8:10 PM schrieb David A Case:
> On Wed, Mar 07, 2018, Carolin Berner wrote:
>> I'm new to Amber and I'm trying to figure out if the amber force fields
>> are suitable for MD simulations at very low temperatures. As the force
>> fields were parametrized for normal conditions, I'm wondering if I
>> shouldn't trust their validity in my simulations.
> There is no general answer to this question, and even few suggestions,
> without knowing more about what types of systems you to studying, what
> you hope to learn, what you mean by "very low temperatures", and so on.
>
> Note that straightforward MD simulations at low temperatures (do you
> mean < 100K?) are usually not very helpful, since "nothing happens":
> everything stays stuck in whatever local minimum you happened to start
> in, as you have very little themal energy to move around.
>
> As a force-field related example, water models developed for the liquid
> will certainly not work well for ice.
>
> One could go on, but I hope you can see the need for more context to
> your question. You should also try to find examples in the literature
> of people who have done simulations along the lines you are thinking
> of--that might provide clues about how to proceed.
>
> ....dac
>
>
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Received on Sun Mar 11 2018 - 01:00:02 PST
