On Tue, Sep 8, 2015 at 10:05 AM, Sergey Samsonov <
sergeys.biotec.tu-dresden.de> wrote:
> Hi Jason,
>
> thanks a lot for your help! Indeed, using HMR with dt = 0.004 for my
> protein (132 aa) increased the speed 1.5 times.
I would have naively expected it to be ~2x faster...
> Applying a cut-off (cut
> = 10) made it 1.5 times faster as well. This is already significant.
>
Yes, but a cutoff of 10 in a GB simulation is really quite horrible. The
electrostatic interactions are far too long-range for 10 A to be a
reasonable cutoff.
>
> Yes, the reason why I wanted to restrain the rest of the protein is that
> I didn't want to have significant deviations from the crystal structure,
> which could lead to unfolding of the protein. But definitely I'll try
> both with and without restraints to see how the global concerted motions
> at longer timescales can be affected by such restraints.
>
Well there are no computational performance implications of applying
either position restraints or constraints.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Sep 08 2015 - 13:30:04 PDT
