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?
Your results can not be judged from this information. Rising energies
from the minimum are fine, as long as they equilibrate to some value
(see tutor example).
But you also say that you get different results with 3.2.1 and 3.3.1, is
that correct?
In that case you can check things by doing two tests:
A: making a tpr file in 3.2.1 and then running it with 3.3.1 and 3.2.1
B: making a tpr in both versions and compare it using gmxcheck -s2 -s1
If A gives you different results then it is a problem, submit a bugzilla.
If B gives you different tpr then check your input.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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