[gmx-users] Energies rising

bharat v. adkar bharat at sscu.iisc.ernet.in
Mon Mar 26 21:42:46 CEST 2007

Dear Sampo,
    rising or lowering of potential energies during md after em seems to be 
fine. energy minimization will optimize for bond-lengths, bond-angles, 
torsion angles to their mean values and try to get rid of any short 
contacts. so basically, em will take ur starting structure to some minimum 
energy structure. however, md will be done at a particular temperature at
which protein might not be at energy minima.. and for most of the 
practical cases, it should not be. so potential energy during md can be 
different than that from em.
    generally, decrease or increase in md pot-energy can depend on the 
choice of minimizer used. conjugate gradient with steepest descent will 
take the structure to the lower energy than with only steepest descent. so 
if you start md after minimization with steep, generally the energy will 
decrease and if it follows minimization with cg-steep, energy will 


On Mon, 26 Mar 2007, Sampo Karkola wrote:

> 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?
> Regards,
> Sampo
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