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.
Regards,
Sampo
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
increase.
bharat
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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