[gmx-users] Energies rising
sampo.karkola at helsinki.fi
Tue Mar 27 07:52:44 CEST 2007
Hi, Bharat and thanks for the answer.
now I'm running an md simulation with the ternary complex (protein,
cofactor, ligand) where the potential energy has risen and stabilised to
a certain level, at least for the first 300 ps. I understand that the
potential energy can rise and I'll be happy if the md finishes nicely.
However, I'm confused with the difference between my earlier
simulations, in which every time the potential energy decreased in the
beginning of the simulation and stabilised. I managed to perform an md
for the cofactor NADP (NDPP topology) where the potential energy
decreased using a different mdp file than earlier, so I think the
problem is in the input, as suggested by David van der Spoel.
I'll try to dig in to the parametrisation of the mdrun.
bharat v. adkar wrote:
> 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?
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