Hi
You have to tell GROMACS in the parameters-file (.ppa) which kind of PMF
you want to calculate (runtype=afm,umbrella). Depending on this choice
it's very likely that the afm_rate is simply ignored for umbrella, no?
The force constant is mimicking the stiffness of the spring. You want to
obey the stiff spring approximation (which still does NOT mean, you
should use a rod ;) ) and therefore shouldn't choose the fc of the
spring to small. I usually use a force constant of 500 kJ/mol*nm^2.
It actually DOES make sense, to choose a fc comparable to the
experiments, you want to compare your sim with, IF you want to compare :)
Hope that helps
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
[EMAIL PROTECTED] wrote:
Dear all,
I have been reading the literature, mailing list and the manual.
There is some questions that I cant understand:
1) there is three methods for the pull code: constraint force, AFM and
umberalla.
in both AFM and Constraint force, there is an option of the rate of
pulling (contraint_rate, AFM_rate), however, for umberalla, there is only
two options, a foce constant and position to be specified!
my question is: how is the pulling controlled in umberalla sampling option?
2) if I want to do an AFM pulling...what is a reasonalble force constant
to use? it seems people are using different K ranging from 10 to 1000's?
thank u
Belquis
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