[gmx-users] Pull code methods?

[Maik Goette]

I'm no umbrella user, but as far as I know, you have to set different 
parameters, according to the manual. These may be similar to the AFM 
parameters, but still, in the config file, they are separated.
Sure, you don't define a pull rate for Umbrella, because you build, as 
you said, discrete systems, where you put the umbrella potential onto 
one group along a reaction coordinate. It's clear that, depending on 
your system, you have to build N systems where your ligand is moved away 
from the protein along the reaction coordinate.

Now, I'm curious about you asking about afm_init again...so you are 
finished with the umbrella business and want to do AFM now?

The sentence, in fact, is very clear. You can break down the statement 
to: Calculate the resulting vector from the difference of two other 
vectors....
Therefore you have to find two vectors. One should be the COM of your 
reference group (you could also choose a single atom there...Just makes 
no sense to me) and one is either the COM of your ligand or, better, one 
single atom of your ligand, where the spring(AFM-tip) is attached to...

I think, this has been discussed in the mailing list more than once...
Maybe you should intensively search the archive for such things...

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:
> 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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> 
> 
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