ahmet yıldırım wrote:
Dear users,
I tried the emol values the following:
As emol=2000, Potential energy=-4.7x10^5
As emol=1000, Potential energy=-4.9x10^5
As emol=100, Potential energy=-5.2x10^5
Generally, when we did the energy minimization:
how much potential energy value=? we can say that the energy
minimization is good.
Potential energy depends on the content of the system, as well as the extent of
minimization. The purpose of EM is to generate a reasonable starting structure
for MD such that the forces do not cause it to explode when you start your
simulation. There is no magical cutoff that determines if you're done; you have
to apply some of the underlying theory to your system and judge that yourself.
-Justin
Thanks in advance
--
Ahmet YILDIRIM
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
