Li, Hualin wrote:
Dear GMX users,
I am using pull code to make a distance restrain to my proteins and
membrane,which looks like this:
pull = umbrella
pull_geometry = cylinder
pull_vec1 = 0 0 1
pull_r1 = 2.5
pull_r0 = 2.5
pull_dim = N N Y ;# 3D
pull_start = yes ;# add COM distance to initial value (initial value =
equilibrium value)
pull_ngroups = 32 ;# excluding the reference
pull_group0 = membrane ;# the reference group - the membrane
pull_pbcatom0 = -1 ;# or -1 - important for PBC of groups larger than half
box,
;# as here for membrane (see manual)
pull_group1 = protein ;# the protein
pull_pbcatom1 = 0 ;# here is no issue since protein is smaller than half
the box
pull_rate1 = 0 ;# do not pull, just maintain distance!
pull_k1 = 800 ;# kJ mol^(-1) nm^(-2)
However, I have 32 protein to keep this local dynamic distance restrain (
pull_geometry = cylinder ), making the calculation goes very slowly. Is
there any method to reduce the frequency to update the dynamic distance check
and restrain please?
If you are maintaining 32 pull groups, your calculations will be horrendously
slow, there's no real way around that without re-writing the code. If you can
do that and maintain accuracy, then the developers are likely to be interested
in it. Otherwise, accept the performance hit.
-Justin
Thank you very much in advance.
Thanks,
Hualin ----
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
--
========================================
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
