[gmx-users] Reduce the frequency to apply distance restrain
Justin A. Lemkul
jalemkul at vt.edu
Mon Oct 10 21:35:30 CEST 2011
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.
> Thank you very much in advance.
> Hualin ----
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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