[gmx-users] temperature explosion...

Eric Jakobsson jake at ncsa.uiuc.edu
Tue May 13 17:48:01 CEST 2003


Another thing that will influence this is how frequently you update the 
pair lists for the direct non-bonded interaction.  The only way to make the 
system truly conservative is to update the pair list every time 
step.  Otherwise I think you will get spurious heating of the sort that you 
describe in constant energy calculations.

Eric



At 02:29 PM 5/12/2003 +0200, you wrote:
>David wrote:
>>On Fri, 2003-05-09 at 17:50, Giorgos Karvounis wrote:
>>
>>>Dear users...
>>>I want to simulate a pentapeptide at 360 K without Tand P coupling. I
>>>first do an equilibration run , starting from a 360K velocity and  T / P
>>>coupling for 100 ps. After that, i switch the coupling and continue the
>>>same run . I monitor the temperature and it seems that it explodes, from
>>>358 to 491 to 651 K every 10000 steps. Is this suppose to happen? Shall
>>>i perform the equilibration longer?
>>>Is it possible to keep the temperature/energy constant without using
>>>coupling?
>>yes, use PME.
>
>You can have a look at J. Comput. Chem. 20, 786-798 (1999) for what
>size of energy drift you can expect at different timestep. Note these
>simulations were done with shifted potentials, to eliminate the cut-off
>noise (hence Davids suggestion for PME, which does nearly as good),
>and in double precision. It depends on how long you want the temperature
>to remain constant, and why you want to run without temperature coupling.
>
>
>--
>Groetjes,
>
>Anton
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>|  _   _  ___,| K. Anton Feenstra                                     |
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---------------------------------
Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Biochemistry
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
405 N. Mathews Avenue
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909






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