On 2/21/13 9:10 PM, Kieu Thu Nguyen wrote:
Dear all,
I can not distinguish when the Fmax < 10 kJmol-1nm-1, < 100, < 1000 ? is
appropriate
Can anyone tell me which value is appropriate for lipid membrane, for
protein in water, for protein in lipid membrane ?
There is no absolute rule. The purpose of EM is just to get the simulation
system into a configuration that is sufficiently relaxed such that dynamics
don't implode. For sensitive free energy calculations and normal mode analysis,
you need the Fmax to be as low as possible. For most protein systems, Fmax <
1000 is generally reasonable for normal MD, but that's just an empirical
observation.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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
