# [gmx-users] Pull code methods?

bmmothan at ucalgary.ca bmmothan at ucalgary.ca
Fri Aug 17 19:47:09 CEST 2007

Hi Maik,

Thank you for the answer. I still have some questions.

I still didn't get the umberalla sampling method. It seems to me AFM and
umberalla are the same except that in umberalla we dont define a Pull
rate. Looking at the literature, people have been using umberalla method
with discrete simulations. i.e. 21 simulation windows. I kind of get the
idea that you will have to manually set up the the 21 discrete simulations
to get the final separated ligand-protein for the umberalla method?
correct me if I am wrong.

The other question I had is about init-afm position option. it says in the
manual:
afm init1 =
Vector describing the initial position of the spring relative to the
reference group. To start a simulation with zero initial force on the
pulled group, the initial position should be set to the position of the
pulled group relative to the reference group.

This sentence is very unclear to me. how do u calculated the poition of
the pulled group relative to the referene.  Is is by calculating the
Center of mass of the pulled group or by calculating the center of mass of
the the whole system (pulled group + reference)?

Thank you,

Belquis

> 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/
>
>
> 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
>>
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