Re: [gmx-users] Umbrella Sampling - Justin tutorial

2011-11-16 Thread Steven Neumann 
Thank you Justin! That helped a lot!

Steven

On Wed, Nov 16, 2011 at 3:06 PM, Justin A. Lemkul  wrote:

>
>
> Steven Neumann wrote:
>
>> Thank you Justin, now I get what you mean!
>> As I understood I should pick just one frame untill 189 ps (when
>> dissociation occured) - does it matter which one I will choose on the final
>> binding free energy?
>>
>
> The free energy minimum should (theoretically) be when the peptides are
> still interacting, i.e. at time zero.  Use this frame and base the spacing
> off of it.
>
>
> Then spacing should be 0.2 nm. Right? But how is it possible to do spacing
>> like this from such results of summary_distances.dat:
>>
>> 189 0.5769072
>>
>> 190 0.5753590
>>
>> 191 0.5711223
>>
>> 192 0.5719844
>>
>> 193 0.5856807
>>
>> 194 0.5886649
>>
>> 195 0.5958101
>>
>> ...
>>
>> 211 0.7111782
>>
>> 212 0.7322708
>>
>> 213 0.7675126
>>
>> ...
>>
>> 378 4.2101626
>>
>> 379 4.1993918
>>
>> 380 4.2223649
>>
>> ..
>>
>> 500 5.48839
>>
>> Do you mean the approximate valueof 0.2 nm spacing? As it would be
>> difficult with these numbers. Can you e.g. do spacing of app. 0.1 nm until
>> e.g. 3 nm and then increase it to 0.2 nm (I think as in your paper) until
>> 5nm?
>>
>>
> Choose approximate values.
>
> My protocol of uneven spacing was necessary to refine the energy minimum
> for the suitable data for the paper.  I kept the tutorial simple; you
> should still achieve a reasonable result.  Uneven spacing is uncommon in
> the literature, so I did not want to give anyone the impression that it was
> a standard protocol, leaving it as an exercise for the reader to understand
> the paper and the motivation for uneven spacing.
>
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
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Re: [gmx-users] Umbrella Sampling - Justin tutorial

2011-11-16 Thread Justin A. Lemkul 



Steven Neumann wrote:

Thank you Justin, now I get what you mean!
As I understood I should pick just one frame untill 189 ps (when 
dissociation occured) - does it matter which one I will choose on the 
final binding free energy?


The free energy minimum should (theoretically) be when the peptides are still 
interacting, i.e. at time zero.  Use this frame and base the spacing off of it.


Then spacing should be 0.2 nm. Right? But how is it possible to do 
spacing like this from such results of summary_distances.dat:
 


189 0.5769072

190 0.5753590

191 0.5711223

192 0.5719844

193 0.5856807

194 0.5886649

195 0.5958101

...

211 0.7111782

212 0.7322708

213 0.7675126

...

378 4.2101626

379 4.1993918

380 4.2223649

..

500 5.48839

Do you mean the approximate valueof 0.2 nm spacing? As it would be 
difficult with these numbers. Can you e.g. do spacing of app. 0.1 nm 
until e.g. 3 nm and then increase it to 0.2 nm (I think as in your 
paper) until 5nm?




Choose approximate values.

My protocol of uneven spacing was necessary to refine the energy minimum for the 
suitable data for the paper.  I kept the tutorial simple; you should still 
achieve a reasonable result.  Uneven spacing is uncommon in the literature, so I 
did not want to give anyone the impression that it was a standard protocol, 
leaving it as an exercise for the reader to understand the paper and the 
motivation for uneven spacing.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Umbrella Sampling - Justin tutorial

2011-11-16 Thread Steven Neumann 
Thank you Justin, now I get what you mean!
As I understood I should pick just one frame untill 189 ps (when
dissociation occured) - does it matter which one I will choose on the final
binding free energy?
Then spacing should be 0.2 nm. Right? But how is it possible to do spacing
like this from such results of summary_distances.dat:


189 0.5769072

190 0.5753590

191 0.5711223

192 0.5719844

193 0.5856807

194 0.5886649

195 0.5958101

...

211 0.7111782

212 0.7322708

213 0.7675126

...

378 4.2101626

379 4.1993918

380 4.2223649

..

500 5.48839

Do you mean the approximate valueof 0.2 nm spacing? As it would be
difficult with these numbers. Can you e.g. do spacing of app. 0.1 nm until
e.g. 3 nm and then increase it to 0.2 nm (I think as in your paper) until
5nm?

Thank you,

Steven


On Wed, Nov 16, 2011 at 2:31 PM, Justin A. Lemkul  wrote:

>
>
> Steven Neumann wrote:
>
>> Hi GMX Users,
>>  I am doing Justin tutorial of Umbrella sampling. I have just finished
>> continous pulling of chainA from the reference chainB. I have some
>> questions. I looked at the trajectory of pulling and it has began with
>> dissociating residue 27Alanine from the ChainB following 26, 25, 24...1. My
>> question is why? As you apply pulling with the constant force to the COM of
>> the whole chain why does it start with terminal residue following then one
>> by one? Why not the middle one or any other?
>>
>>
>
> By pulling on the COM of any molecule, the forces are then redistributed
> to the other atoms.  In the case given in the tutorial, the region you see
> dissociate first is held together by relatively weak interactions.  If you
> pull directly on a specific residue or atom, that residue will dissociate
> first in all likelihood.  For further discussion pertinent to this specific
> system, please refer to our paper linked from the tutorial.  You're
> observing what we observed, so there is no problem and I am happy that the
> behavior is reproducible for others :)
>
>
> The second thing I would like to extract starting configurations from from
>> my pulling. Till frame 189 the COM varies from 0.49 to 0.56 - makes sense
>> as the ChainA is still within ChainB. I would like to use configurations:
>>  0 - 0.50
>> 50 - 0.52
>> 100 - 0.51
>> 150 - 0.51
>> 200 - 0.62
>> 250 - 2.21
>> 
>> 500 - 5.48
>>  My question is: Do I have to use exactly the same e.g. 0.2 nm spacing or
>> this configuration above is ok? Can the spacing in nm vary?
>>
>
> I'm not clear on what you mean here.  In constructing a reaction
> coordinate, you need to sample at finite intervals along the given path.
>  0.2 nm is a common spacing used for many systems, and if you want to
> reproduce the tutorial's results, you should use that spacing.  Otherwise,
> I can't guarantee what you will see.  The peptide chains remain bound for a
> long time, until the force applied by the harmonic spring overcomes the
> intermolecular interactions.  This was useful in our study (again, see the
> paper for why).
>
>
> And the last thing - is it required to use frames till 189 as the COM
>> varies in this area?
>>
>>
>
> You only need one to represent the center of that particular window, since
> the COM distance isn't changing much here.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
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Re: [gmx-users] Umbrella Sampling - Justin tutorial

2011-11-16 Thread Justin A. Lemkul 



Steven Neumann wrote:

Hi GMX Users,
 
I am doing Justin tutorial of Umbrella sampling. I have just finished 
continous pulling of chainA from the reference chainB. I have some 
questions. I looked at the trajectory of pulling and it has began with 
dissociating residue 27Alanine from the ChainB following 26, 25, 24...1. 
My question is why? As you apply pulling with the constant force to the 
COM of the whole chain why does it start with terminal residue following 
then one by one? Why not the middle one or any other?
 


By pulling on the COM of any molecule, the forces are then redistributed to the 
other atoms.  In the case given in the tutorial, the region you see dissociate 
first is held together by relatively weak interactions.  If you pull directly on 
a specific residue or atom, that residue will dissociate first in all 
likelihood.  For further discussion pertinent to this specific system, please 
refer to our paper linked from the tutorial.  You're observing what we observed, 
so there is no problem and I am happy that the behavior is reproducible for 
others :)


The second thing I would like to extract starting configurations from 
from my pulling. Till frame 189 the COM varies from 0.49 to 0.56 - makes 
sense as the ChainA is still within ChainB. I would like to use 
configurations:
 
0 - 0.50

50 - 0.52
100 - 0.51
150 - 0.51
200 - 0.62
250 - 2.21

500 - 5.48
 
My question is: Do I have to use exactly the same e.g. 0.2 nm spacing or 
this configuration above is ok? Can the spacing in nm vary?


I'm not clear on what you mean here.  In constructing a reaction coordinate, you 
need to sample at finite intervals along the given path.  0.2 nm is a common 
spacing used for many systems, and if you want to reproduce the tutorial's 
results, you should use that spacing.  Otherwise, I can't guarantee what you 
will see.  The peptide chains remain bound for a long time, until the force 
applied by the harmonic spring overcomes the intermolecular interactions.  This 
was useful in our study (again, see the paper for why).


And the last thing - is it required to use frames till 189 as the COM 
varies in this area?
 


You only need one to represent the center of that particular window, since the 
COM distance isn't changing much here.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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[gmx-users] Umbrella Sampling - Justin tutorial

2011-11-16 Thread Steven Neumann 
Hi GMX Users,

I am doing Justin tutorial of Umbrella sampling. I have just finished
continous pulling of chainA from the reference chainB. I have some
questions. I looked at the trajectory of pulling and it has began with
dissociating residue 27Alanine from the ChainB following 26, 25, 24...1. My
question is why? As you apply pulling with the constant force to the COM of
the whole chain why does it start with terminal residue following then one
by one? Why not the middle one or any other?

The second thing I would like to extract starting configurations from from
my pulling. Till frame 189 the COM varies from 0.49 to 0.56 - makes sense
as the ChainA is still within ChainB. I would like to use configurations:

0 - 0.50
50 - 0.52
100 - 0.51
150 - 0.51
200 - 0.62
250 - 2.21

500 - 5.48

My question is: Do I have to use exactly the same e.g. 0.2 nm spacing or
this configuration above is ok? Can the spacing in nm vary?
And the last thing - is it required to use frames till 189 as the COM
varies in this area?

Thank you!

Steven
-- 
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