[gmx-users] Themostat problem

Eric Jakobsson jake at ncsa.uiuc.edu
Thu Oct 23 18:50:01 CEST 2003

I think your time constant is too short, so that you are making way too big 
corrections to the velocity on each time step.  It doesn't look so bad for 
the water because there are so many waters so that errors are averaging, 
but with just a few ions you are getting very big fluctuations.


At 10:43 AM 10/22/2003 -0500, qiao rui wrote:
>Dear All:
>         I am trying to use Nose-Hoover thermostat for my simulation
>system, where I have ~1500 water molecules, ~50 Na+ and ~50~ Cl- ions. I
>used the following paramters:
>         tau_t = 0.05 ps; t_ref = 300K for each group.
>         Using g_energy, I got the following statistics:
>Energy             Average       RMSD     Fluct.      Drift  Tot-Drift
>T-SOL              300       4.91058    4.90895 -0.000912265   -0.437889
>T-Na               300.003   279.733    243.602   0.992376    476.343
>T-Cl               299.997    385.632    373.082    0.70422    338.027
>         It seems that the fluctuation of the temperature for Na+ and Cl-
>is huge. Is there some way to solve the problem?
>         Another question I have is: is it possible to just couple the x-
>and y- degree of freedom with the themostat instead of coupling all the
>three directions to the thermostat?
>         sincerely,
>         Rui Qiao
>Rui Qiao
>Research Assistant
>Beckman Institute, UIUC
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Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909
(Currently on leave to the National Institutes of Health in Bethesda, 
Maryland, to be Director of the NIGMS Center for Bioinformatics and 
Computational Biology and Chair of the NIH Biomedical Information Science 
and Technology Initiative Consortium, but maintaining my research lab at 
Illinois by periodic commuting.  My usual schedule is four days a week at 
NIH and three days a week at Illinois.)

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