Justin A. Lemkul wrote:
ERIKSSON, EMMA wrote:
I was using those "strange" values of tau_p and compressibility to
keep the z
box length fixed in order to avoid problems associated with scaling the
positions of the molecules in the box when we constrain the distance
between
DPPC and the small molecule. I was told to use those values but maybe
it's
not correct...
I would certainly try to eliminate it as a possibility. I just don't
know how the pressure coupling algorithm could possibly handle a tau_t
that is several 10e-11 times smaller than the timestep!
*Edit* That should read "tau_p."
A well-equilibrated system should not fluctuate substantially over the
course of a simulation, anyway. But if you need to fix the box, you
*may* be able to set the relevant values of tau_t and compressibility to
*Edit* This should also read "tau_p."
zero (as in the case of tau_t for temperature coupling), but I have
never tried it.
This one's right :) Apologies for any confusion, my brain was going faster than
my fingers on this reply!
-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
========================================
--
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/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/mailing_lists/users.php
