James Starlight wrote:
Mark,
2011/10/26 Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
Or that your starting structure is not close enough to a sensible
minimum for a local gradient-based optimizer to do the job. Look at
the atoms with the large forces and see what you can learn.
So for that purpose I've done steep minimization first and only that
based on that minimized structure I did CG minimization. I changed the
emtool ( from 100 to 1000) as well as step size but my structure always
have not been prorely minimized ( based on the system output ). Also
I've found that there is third L-BFGS
<http://www.gromacs.org/Documentation/Terminology/L-BFGS> algorithm for
minimization. In what cases this minimization could be helpfull?
You should probably be using it.
http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis
Note that increasing emtol from 100 to 1000 actually makes your results worse,
since mdrun will stop when the maximum force is below 1000 kJ/mol-nm, which is
orders of magnitude too high for NMA.
-Justin
Sorry, we can't make guesses based on things you can't remember
details about. Maybe you want to consider Essential Dynamics.
As I know the Essential dynamics is the type of the PC analysis ( in
this case the ensemble of the analysed structures is replaced by the
ensemble of the MD snapshots ). But I've heard that there is possible
ways to extract normal modes indirectly from the output trajectories.
James
--
========================================
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
