[gmx-users] Pull code methods?

Maik Goette mgoette at mpi-bpc.mpg.de
Thu Aug 16 10:52:42 CEST 2007


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


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

bmmothan at ucalgary.ca 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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> .

More information about the gromacs.org_gmx-users mailing list