Mark Abraham wrote:
On 25/05/11, *郭漫 * <[email protected]> wrote:
Hello users,
I followed the tutorial steps to do umbrella sampling of GROMACS
Tutorial, (This is the tutorial site
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html)
and get the PMF is close to -50 kcal/mol. However, when I put
amber99sb parameter instead of gromos96 53a6 parameter, without
changing the other parameters and steps，the result is about -35
kcal/mol. I don't know why the difference is so large between them,
and i need your help for explaining what is the reason for the
difference, simply because I changed the force filed, or some other
possible causes.
If all you've changed is the force field, and these simulations are long
enough to produce converged measurements, then "welcome to the jungle".
Different force fields have been demonstrated to be good or bad on
different types of systems for different types of properties. Choosing
the right force field is normally a most important and sometimes the
most time-consuming part of doing simulations properly. Read widely, and
take good notes.
Agreed. Also important to note is that simply changing the force field and not
adjusting any of the .mdp settings (as would be required for proper use of a
different force field) could result in incorrect use of the new force field. I
don't often use the Amber force fields, but I believe different cutoffs and
neighborsearching intervals should be used. The parameters given are for Gromos96.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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