[gmx-users] Re: Re: energy decreasing in NVE simulation

Yan Yun-an yun-an.yan at uni-rostock.de
Thu May 20 13:05:52 CEST 2010

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  

 >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  
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  
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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