The force acting on your pulled group is:
F=k(vt-x)
where x is the displacment of that group (1) relativ to group (0).
I thin Justin used this values to create the structure for the later
umbrella sampling, so the pulling velocity is rather fast.
I usually used k1=500, and velocities of about 0.001 to 0.0001 for
pulling experiment for systems with only a few hydrogen bonds.
I think the choice of the parameters depends upon how strong your
molecules interact with another.
But for umbrella sampling i would assume that it matters most that you
generate strucutres with the right distance and not so much with what
pulling velocity you reached this distances.
Greetings
Thomas
Hi Justin
Thanks for your help. The two molecules are now moving together. I am
however slightly confused about the parameters pull_rate1 and pull_k1. I
want the molecules to come together very slowly therefore
I would set the rate to be a very small value. How the does the force
come into play and how should you decide on the best value?
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Hi Justin
Thanks. If I use the pull_geometry = direction I would go for the
following jus t to pull the molecules together in the z direction.
pull = umbrella
pull_geometry = direction
pull_start = yes
pull_ngroups = 1
pull_group0 = cage_1
pull_group1 = cage_2
pull_vec1 = 0.0 0.0 -1.0
pull_rate1 = 0.01
pull_k1 = 1000
Does this seem reasonable? Also in the pull_rate what is meant by the
Probably. Try it.
'rate of change of the reference position'? (Is it the position of the
reference group, if so what if I don't want it to change?)
It is the rate of change of the reference position, which is the
position at the outset of the simulation. Your objective is to pull
your two species together, right? I don't see why you wouldn't want
it to change. You're not changing anything about pull_group0 (your
reference group), since you aren't setting pull_rate0. Everything is
applied to pull_group1 (hence _rate1, _k1, etc).
-Justin
Cheers
Gavin
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