[gmx-users] Energies rising

Sampo Karkola sampo.karkola at helsinki.fi
Mon Mar 26 08:14:08 CEST 2007

Dear list,

earlier I posted a message on the list about rising energies in md 
simulation and I still have not found a solution (see a thread with the 
header "incomparable results with files	produced with gromacs3.2.1 and 
3.3.1"). I observed that the energies rise in any simulation I'm trying, 
i.e. any ligand or protein whether simulated in complex or alone. I got 
one suggestion that the temperature (entropy) could be the reason for 
weird behaviour of the potential energy. I'm simulating at 310K, and I 
studied the effect of the temperature and found the following:

-at 50 K the potential energy decreases as it should  and as it has done 
earlier at 310K

-at 200K the potential energy rises immediately at the beginning, but 
after 0.2 ps, the energy decreases below the starting point

-at 250 the potential energy rises and stays high

I would like to simulate the system at body temperature. Any suggestions 
how to do that?



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