if it's already equilibrated at 300K, I would heat from that T instead of
cooling it to 0K first.
However, I would also be very cautious in interpreting high temperature
unfolding as being representative of anything happening at biological T.
On Fri, Apr 24, 2015 at 10:17 AM, Biswa Ranjan Meher <brmeher2013.gmail.com>
wrote:
> Dear Amber Users,
>
> I would like to carry out a simulation of the protein of interest at high
> temperature (425K) with TIP3P solvent to understand the unfolding process.
> The starting structure for the 425K simulation is a stable PDB structure
> extracted from an MD simulation performed earlier at 300K.
>
> My question is that, for the high temperature simulation, whether I would
> heat the protein (PDB from 300K simulation) from 0 K - 425 K in step wise
> OR simply start from 300K to reach up to 425 K.
>
> Any suggestions is highly appreciated.
>
> Thanks
> Biswa
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Received on Fri Apr 24 2015 - 07:30:04 PDT
