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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