[gmx-users] re: temp explosion and shifted potentails

George Karvounis gk237 at cam.ac.uk
Tue May 13 12:32:02 CEST 2003

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

> 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

Dear Anton,

thank you for this ref. The simulation i want to run i pretty long (40 
ns) , it is actually a simulation has been done in the past by the 
Gromacs group, the folding of a beta-hairpin, from the extended 
configuration at 360 K. The reasons that i dont want to use coupling are 
technical and not physical. Due to a special kind of statistical 
analysis we want to apply, we need to be able to go back to the 
simulation and reproduce several frames of critical moments. I 
understood (and experienced) that this is not possible when coupling 
(either T or P) is on, of course when i use coulomb. When i run an 
equilibration run and then switch the coupling off,explosion takes 
place. Then i used PME, i can now reproduce the frames (i.e. get same 
coordinates and velocities) but i get the energy drift and the temp is 
dropping down...
I was not familiar with the shifted potentials, but if the coupling 
stays off, then i think they might be a solution to our problems

Thanks a lot


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