Hi, David
I would say harm=100 could be better, since a smaller strength and slower
speed
always make the steering more smooth. Actually, in my SMD for various of
systems
harm = 100 could be a little bit large, I recommend to use smaller harm
strength to try.
The SPLINE gives the SMD along the path which is spline interpolated by the
given path points.
Always the SPLINE could be better than LINE since it is more smooth, but
they shouldn't result in
big differences.
Best
Feng
On Fri, Feb 2, 2018 at 9:29 AM, David Sáez <davidsaez.udec.cl> wrote:
> Hi.
>
> I am trying to generate structures for umbrella sampling pulling a bond
> with the SMD tools available in Sander (AT17, Amber16). I tried pulling
> with two difference force constants defined by "harm=100" and "harm=200". I
> obtained different results for the final structures and work profiles.
>
> Besides that, I don't understand very well the meaning of the path_mode
> variable. In my simulation I just provide the initial and final points of
> the DISTANCE CV (just 2 points) and set it to 'LINES'. Should I expect a
> different behavior if set it to 'SPLINE'?
>
> Regards
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>
--
Feng Pan
Ph.D.
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Sat Feb 03 2018 - 17:00:02 PST
