Justin A. Lemkul wrote:
Lara Bunte wrote:
Hello
Is this em.mdp file correct for a simple MD simulation?
integrator = steep
nsteps = 200
nstlist = 10
You should set nstlist=1 for energy minimization (which is not, by
definition, MD).
Hit "send" too soon...
You have also specified 200 steps. This seems arbitrary to me, as there is no
guarantee that EM will be done at that point. You also need to specify a value
for emtol and emstep to be more effective.
There are tutorials linked from the Gromacs webpage. I'd suggest you work
through at least one or two of them to understand what the .mdp files are trying
to achieve and what a proper workflow might be.
-Justin
rlist = 1.0
coulombtype = pme
rcoulomb = 1.0
vdw-type = cut-off
rvdw = 1.0
nstenergy = 10
Thanks for help
Greetings
Lara
--
========================================
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 [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
