Dear Erik,
Thank you so much for your prompt reply. I appreciate it.
Yun-an Yan
Erik Marklund writes:
>For more exotic NVE-systems I had to do some or several of the
following
>things to get stable Etot:
>* have an even shorter timestep than one would expect from the applied
>constraints and such.
I will try a timestep with 0.5 fs.
>* use double precision.
The double precision is already in use.
>* apply the constraints with lower tolerance/more iterations etc.
I thought shake_tol = 1.e-8 is small enough. May I try an even
smaller value?
Or the lincs algorithm with lincs_order=8 and lincs_iter=2 is
recommended
instead of shake?
>Then there's a few things I notice in your setup:
>* I see that you do not use constrints at all. I would give it a shot.
I will try.
>* Why do you have two separate comm-grps?
Since it is a solute-solvent fashion MD, I am trying to keeping the
solute
part close the center of the simulation box. But it does not work in
this way.
Do you have any idea about that?
>Erik Marklund
>
>--
>-----------------------------------------------
>Erik Marklund, PhD student
>Dept. of Cell and Molecular Biology, Uppsala University.
>Husargatan 3, Box 596, 75124 Uppsala, Sweden
>phone: +46 18 471 4537 fax: +46 18 511 755
>erikm at xray.bmc.uu.se http://folding.bmc.uu.se/
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