Sampo Karkola wrote:
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.
You may also want to reflect on your input. Sometimes you can see the
energy go down, for instance when you have a system at low density that
contracts, and sometimes it can go up, e.g. when you start at 0 K and
increase the T. If you generate velocities in grompp the rise should not
at all be so high. I don't think the force field is the problem here.
--
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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