subject:"\[gmx\-users\] pull\-code"

Yes, the pulling is in all direction. But i tried to explain it in one 
dimension.

Lol, send last mail only to Gavin.

The real problem (i think) is the following:
We have our pulled group  1nm right from the reference group, and the 
umbrella potential is also centered the (we used pull_start=yes, or 
pull_init=1).

The umbrella force is zero.

Now we move the particle 2nm to the left, to we have the same distance, 
but into the left direction. Since the distance is the same, the 
umbrella force is zero. On its way the umbrella force increases, maximum 
when the pulled group is on top of the reference group, and then 
decreases back to zero.
But we wanted a potential, where it doesn't matter if the particle moves 
to the left or right, force should always increase. But with 
pull_geometry=distance we can't get it.
If the distances between reference and pulled group are big enough we 
don't run into this problem.


--

Hello,

I was following your argument but then doesnt pull_dim=Y Y Y mean it 
pulls in all directions at once?  I use pull_dim=N N Y , or just 1 pull 
direction and it works.  I might be wrong, but would be interesting if 
you got it to work like that for a small molecule.


Stephan Watkins

 Original-Nachricht 
> Datum: Fri, 17 Feb 2012 16:34:22 +0100
> Von: Thomas Schlesier 
> An: gmx-users at gromacs.org
> Betreff: [gmx-users] pull-code

> Hi Gavin,
> if i remember correctly it was a system about pulling a ligand from a
> binding pocket?
> To make the system simpler we have a big circle and in the middle a
> small circle. And we assume that the potential minimum for the
> interaction between both circles is when the small cirlce is in the
> middle of the large circle.
> Now we do the Umbrella sampling. For a window which is centered at a
> distance which is sligthly greater then 0, we will get problems. Assume
> small circle is sligthly shifted to the right. And the other windows are
> also in this dircetion. (-> reaction coordinate goes from zero to the
> right dircetion)
> If the small circle moves between 0 and any value <0 everythig should be
> fine. But if the small circle moves to the left, we will also get a
> positive distance. Problem is from the above defined reaction coordinate
> it should be a negative distance. So we are counting the positive
> distances too much.
> To check this, you could use *g_dist* to calculate the distance for both
> molecules for the problematic windows. Then project the resulting vector
> onto your reaction coordinate. Then you should see the crossings between
> the right and left side.
>
> How do the two free energy curves compare for larger distances, where
> you can be sure, that you do not have this 'crossing problem'?
>
> Greetings
> Thomas
>
>
>
> 
-

>
>
> Hi all
>
> I am returning to a query I had a few weeks ago regarding a discrepancy
> between two free energy curves. One calculated using umbrella sampling,
> the other calculated via the reversible work theorem from the RDF. There
> is sufficient sampling of the dynamics in the RDF so this method is
> viable.
> Anyway in the pull-code I use pull_geometry = dist and pull_dim=Y Y Y.
> The free energy curve from the pull-code method does not give me a
> minimum at the zero value of the order parameter whereas the RDF method
> does. Someone said before about double counting of positive distances at
> small values of the order parameter and therefore information is lost at
> very small distances.
>
> Is this correct?
> I am slightly concerned that my curves are not giving me the correct
> information involving a very important state in my reaction coordinate.
>
> Also when this dist restraint (which cannot be negative) is implemented
> are there issues with the normalisation of the histograms from g_wham?
>
> Cheers
>
> Gavin
>
>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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Re: [gmx-users] pull-code

2012-02-17 Thread lloyd riggs

Hello,

I was following your argument but then doesnt pull_dim=Y Y Y mean it pulls in 
all directions at once?  I use pull_dim=N N Y , or just 1 pull direction and it 
works.  I might be wrong, but would be interesting if you got it to work like 
that for a small molecule.

Stephan Watkins

 Original-Nachricht 
> Datum: Fri, 17 Feb 2012 16:34:22 +0100
> Von: Thomas Schlesier 
> An: gmx-users@gromacs.org
> Betreff: [gmx-users] pull-code

> Hi Gavin,
> if i remember correctly it was a system about pulling a ligand from a 
> binding pocket?
> To make the system simpler we have a big circle and in the middle a 
> small circle. And we assume that the potential minimum for the 
> interaction between both circles is when the small cirlce is in the 
> middle of the large circle.
> Now we do the Umbrella sampling. For a window which is centered at a 
> distance which is sligthly greater then 0, we will get problems. Assume 
> small circle is sligthly shifted to the right. And the other windows are 
> also in this dircetion. (-> reaction coordinate goes from zero to the 
> right dircetion)
> If the small circle moves between 0 and any value <0 everythig should be 
> fine. But if the small circle moves to the left, we will also get a 
> positive distance. Problem is from the above defined reaction coordinate 
> it should be a negative distance. So we are counting the positive 
> distances too much.
> To check this, you could use *g_dist* to calculate the distance for both 
> molecules for the problematic windows. Then project the resulting vector 
> onto your reaction coordinate. Then you should see the crossings between 
> the right and left side.
> 
> How do the two free energy curves compare for larger distances, where 
> you can be sure, that you do not have this 'crossing problem'?
> 
> Greetings
> Thomas
> 
> 
> 
> -
> 
> 
> Hi all
> 
> I am returning to a query I had a few weeks ago regarding a discrepancy
> between two free energy curves. One calculated using umbrella sampling,
> the other calculated via the reversible work theorem from the RDF. There
> is sufficient sampling of the dynamics in the RDF so this method is
> viable.
> Anyway in the pull-code I use pull_geometry = dist and pull_dim=Y Y Y.
> The free energy curve from the pull-code method does not give me a
> minimum at the zero value of the order parameter whereas the RDF method
> does. Someone said before about double counting of positive distances at
> small values of the order parameter and therefore information is lost at
> very small distances.
> 
> Is this correct?
> I am slightly concerned that my curves are not giving me the correct
> information involving a very important state in my reaction coordinate.
> 
> Also when this dist restraint (which cannot be negative) is implemented
> are there issues with the normalisation of the histograms from g_wham?
> 
> Cheers
> 
> Gavin
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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[Fwd: Re: [gmx-users] pull-code]


--- Begin Message ---
Hi Thomas

I am sorry to bother you but if you could answer a few questions I have
about how the pull-code works with respect to my system I would really
appreciate it.
My system is a liquid and I am trying to pull one substituent of one
liquid molecule in a certain region of another liquid molecule using as
I said earlier pull_geometry =dist and pull_dim =YYY.
Also pull_start = no
Say I have a window with pull_init=0

1) At the very start of the simulation the pullcode calculates the
vector between the two groups? Is there anything particularly
significant about this initial vector? Is this distance vector
recalculated at every step?
2) Does it compare the distance vector an time t with that at time 0.?
3) Given the initial vector can this vector change (i.e. dierection) or
does the distance between the two groups vary only along this vector
(i.e. in a line) ?

Cheers

Gavin


Thomas Schlesier wrote:
> Hi Gavin,
> if i remember correctly it was a system about pulling a ligand from a
> binding pocket?
> To make the system simpler we have a big circle and in the middle a
> small circle. And we assume that the potential minimum for the
> interaction between both circles is when the small cirlce is in the
> middle of the large circle.
> Now we do the Umbrella sampling. For a window which is centered at a
> distance which is sligthly greater then 0, we will get problems.
> Assume small circle is sligthly shifted to the right. And the other
> windows are also in this dircetion. (-> reaction coordinate goes from
> zero to the right dircetion)
> If the small circle moves between 0 and any value <0 everythig should
> be fine. But if the small circle moves to the left, we will also get a
> positive distance. Problem is from the above defined reaction
> coordinate it should be a negative distance. So we are counting the
> positive distances too much.
> To check this, you could use *g_dist* to calculate the distance for
> both molecules for the problematic windows. Then project the resulting
> vector onto your reaction coordinate. Then you should see the
> crossings between the right and left side.
>
> How do the two free energy curves compare for larger distances, where
> you can be sure, that you do not have this 'crossing problem'?
>
> Greetings
> Thomas
>
>
>
> -
>
>
>
> Hi all
>
> I am returning to a query I had a few weeks ago regarding a discrepancy
> between two free energy curves. One calculated using umbrella sampling,
> the other calculated via the reversible work theorem from the RDF. There
> is sufficient sampling of the dynamics in the RDF so this method is
> viable.
> Anyway in the pull-code I use pull_geometry = dist and pull_dim=Y Y Y.
> The free energy curve from the pull-code method does not give me a
> minimum at the zero value of the order parameter whereas the RDF method
> does. Someone said before about double counting of positive distances at
> small values of the order parameter and therefore information is lost at
> very small distances.
>
> Is this correct?
> I am slightly concerned that my curves are not giving me the correct
> information involving a very important state in my reaction coordinate.
>
> Also when this dist restraint (which cannot be negative) is implemented
> are there issues with the normalisation of the histograms from g_wham?
>
> Cheers
>
> Gavin
>
>

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[gmx-users] pull-code

Hi Gavin,
Justin wrote some stuff in a nice tutorial for the different 
pull_geometry options. I think i saw the link today or yesterday in one 
of his messages, but i can't find it on his tutorial page :(

So we have a reference (ref) pulled group (pgrp) and a spring (center / 
minimum of the pulling potential).
The position of the spring is relative to ref and is affected by 
pull_init (-> also pull_start) and the pull_vector. If pull_init=0 the 
spring has at t=0 the same position as the ref-group.

With pull_init=0 and pull_start=yes, the spring would be centered at the 
position of pgrp.

Then we have 3 pull_geometries:

distance:
We pull along the vector which connects ref and pgrp. So pull_init=x, 
x>0  would mean the spring is, spring is x nm away from ref, along the 
vector connecting ref and pgrp. With time the spring will move further 
along this vector. The pull_vector should be calculated at everytime 
step. So if the system rotates, the pull_vector would also rotate.

dircetion:
Same as distance, but we have a fixed pull_vector.
So if the system rotates, the pull_vector will not rotate.
pull_init is also along this pull_vector.

position:
Same as dircetion,
but pull_init can be freely chosen (meaning, it is not related to the 
pull_vector)

Since the position of the spring is always related to the position of 
the reference group, we will get no problems due to moving of ref -> 
spring would move the same way. So we can say, for the pulling, ref is 
fixed and the spring move from the position defined by pull_init along 
the pull_vector.

Hope this answers your question and gives a little bit more 
understanding about the pull-code.

One thing concerning PBC:
If i understand it correctly, for PBC the distance between ref and pgrp 
is relevant. and not the distance between the spring and ref or pgrp.

Greetings
Thomas

---

Hi Thomas

I am sorry to bother you but if you could answer a few questions I have
about how the pull-code works with respect to my system I would really
appreciate it.
My system is a liquid and I am trying to pull one substituent of one
liquid molecule in a certain region of another liquid molecule using as
I said earlier pull_geometry =dist and pull_dim =YYY.
Also pull_start = no
Say I have a window with pull_init=0

1) At the very start of the simulation the pullcode calculates the
vector between the two groups? Is there anything particularly
significant about this initial vector? Is this distance vector
recalculated at every step?
2) Does it compare the distance vector an time t with that at time 0.?
3) Given the initial vector can this vector change (i.e. dierection) or
does the distance between the two groups vary only along this vector
(i.e. in a line) ?

Cheers

Gavin

Thomas Schlesier wrote:
> Hi Gavin,
> if i remember correctly it was a system about pulling a ligand from a
> binding pocket?
> To make the system simpler we have a big circle and in the middle a
> small circle. And we assume that the potential minimum for the
> interaction between both circles is when the small cirlce is in the
> middle of the large circle.
> Now we do the Umbrella sampling. For a window which is centered at a
> distance which is sligthly greater then 0, we will get problems.
> Assume small circle is sligthly shifted to the right. And the other
> windows are also in this dircetion. (-> reaction coordinate goes from
> zero to the right dircetion)
> If the small circle moves between 0 and any value <0 everythig should
> be fine. But if the small circle moves to the left, we will also get a
> positive distance. Problem is from the above defined reaction
> coordinate it should be a negative distance. So we are counting the
> positive distances too much.
> To check this, you could use *g_dist* to calculate the distance for
> both molecules for the problematic windows. Then project the resulting
> vector onto your reaction coordinate. Then you should see the
> crossings between the right and left side.
>
> How do the two free energy curves compare for larger distances, where
> you can be sure, that you do not have this 'crossing problem'?
>
> Greetings
> Thomas
>
>
>
> 
-

>
>
>
> Hi all
>
> I am returning to a query I had a few weeks ago regarding a discrepancy
> between two free energy curves. One calculated using umbrella sampling,
> the other calculated via the reversible work theorem from the RDF. There
> is sufficient sampling of the dynamics in the RDF so this method is
> viable.
> Anyway in the pull-code I use pull_geometry = dist and pull_dim=Y Y Y.
> The free energy curve from the pull-code method does not give me a
> minimum at the zero value of the order parameter whereas the RDF method
> does. Someone said before about double counting of positive distances at
> small values of the order parameter and there

Re: [gmx-users] pull-code

Hi Thomas

A few points below under your points

Thomas Schlesier wrote:
> Yes you are right, should be between 0 and >0.
>
> Do you have a window for a distance equal 0?
Yes
>
>
> This window should behave similar to the RDF-analysis. Because there
> are "no directions".

It doesn't. By this I mean the zero point of the reaction coordinate
does not give  a free energy minimum (actually the minimum is shifted to
the right) whereas from the reversible work theorem it does.
>
> Or to reformulate the problem.
> We make an umbrella window for a distance of 1. If particle stays
> there everything is fine. If particle moves to 0, it should be also
> fine (particle sees a force of k*1). If paticle moves to -1, it should
> see a force of k*2, but instead, the distance is 0 -> no force.
I don't understand from "if particle moves .."
> If you have the umbrella window centered at 0 this problem vansihes ->
> if particle move it sees always a force.
>
> But one thing gives me headaches. I don't have this problem in my
> pulling simulation, because the distance between my reference and
> pulled group can not become zero:
> But concerning the reaction coordinate it will have a similar flaw
> like the RDF i think: It doesn't matter in wish direction the particle
> moves (left or right) due to the distance we would always say it moves
> along the reaction coordinate. In reality it moves sometimes in the
> negative direction of the reaction coordinate, but we always say it's
> a positve distance -> so positive value on the reaction coordinate.
> For an isotropic system this would not matter, but for system which we
> have a anisotrop reaction coordinate it should matter.
My system is isotropic
>
>
> Greetings
> Thomas
>
>
>
> Am 17.02.2012 17:07, schrieb gmx-users-requ...@gromacs.org:
>> Hi Thomas Many thanks for the reply again. At larger distances the two
>> curves match up quite well. The curve from the reversible work theorem
>> is better behaved and smoother but this could be solely due to
>> statistics. I am slightly confused about your statement "If the small
>> circle moves between 0 and any value <0 everything should be fine." Do
>> you not mean 0 and any value >0 ? Cheers Gavin Thomas Schlesier wrote:
>>> >  Hi Gavin,
>>> >  if i remember correctly it was a system about pulling a ligand
>>> from a
>>> >  binding pocket?
>>> >  To make the system simpler we have a big circle and in the middle a
>>> >  small circle. And we assume that the potential minimum for the
>>> >  interaction between both circles is when the small cirlce is in the
>>> >  middle of the large circle.
>>> >  Now we do the Umbrella sampling. For a window which is centered at a
>>> >  distance which is sligthly greater then 0, we will get problems.
>>> >  Assume small circle is sligthly shifted to the right. And the other
>>> >  windows are also in this dircetion. (->  reaction coordinate goes
>>> from
>>> >  zero to the right dircetion)
>>> >  If the small circle moves between 0 and any value<0 everythig should
>>> >  be fine. But if the small circle moves to the left, we will also
>>> get a
>>> >  positive distance. Problem is from the above defined reaction
>>> >  coordinate it should be a negative distance. So we are counting the
>>> >  positive distances too much.
>>> >  To check this, you could use*g_dist*  to calculate the distance for
>>> >  both molecules for the problematic windows. Then project the
>>> resulting
>>> >  vector onto your reaction coordinate. Then you should see the
>>> >  crossings between the right and left side.
>>> >
>>> >  How do the two free energy curves compare for larger distances,
>>> where
>>> >  you can be sure, that you do not have this 'crossing problem'?
>>> >
>>> >  Greetings
>>> >  Thomas
>>> >
>>> >
>>> >
>>> > 
>>> -
>>>
>>> >
>>> >
>>> >
>>> >  Hi all
>>> >
>>> >  I am returning to a query I had a few weeks ago regarding a
>>> discrepancy
>>> >  between two free energy curves. One calculated using umbrella
>>> sampling,
>>> >  the other calculated via the reversible work theorem from the
>>> RDF. There
>>> >  is sufficient sampling of the dynamics in the RDF so this method is
>>> >  viable.
>>> >  Anyway in the pull-code I use pull_geometry = dist and pull_dim=Y
>>> Y Y.
>>> >  The free energy curve from the pull-code method does not give me a
>>> >  minimum at the zero value of the order parameter whereas the RDF
>>> method
>>> >  does. Someone said before about double counting of positive
>>> distances at
>>> >  small values of the order parameter and therefore information is
>>> lost at
>>> >  very small distances.
>>> >
>>> >  Is this correct?
>>> >  I am slightly concerned that my curves are not giving me the correct
>>> >  information involving a very important state in my reaction
>>> coordinate.
>>> >
>>> >  Also when this dist restraint (which cannot be negative) is
>>> implemented
>>> >  are there issues with

[gmx-users] pull-code

Yes you are right, should be between 0 and >0.

Do you have a window for a distance equal 0?

This window should behave similar to the RDF-analysis. Because there are 
"no directions".

Or to reformulate the problem.
We make an umbrella window for a distance of 1. If particle stays there 
everything is fine. If particle moves to 0, it should be also fine 
(particle sees a force of k*1). If paticle moves to -1, it should see a 
force of k*2, but instead, the distance is 0 -> no force.
If you have the umbrella window centered at 0 this problem vansihes -> 
if particle move it sees always a force.

But one thing gives me headaches. I don't have this problem in my 
pulling simulation, because the distance between my reference and pulled 
group can not become zero:
But concerning the reaction coordinate it will have a similar flaw like 
the RDF i think: It doesn't matter in wish direction the particle moves 
(left or right) due to the distance we would always say it moves along 
the reaction coordinate. In reality it moves sometimes in the negative 
direction of the reaction coordinate, but we always say it's a positve 
distance -> so positive value on the reaction coordinate.
For an isotropic system this would not matter, but for system which we 
have a anisotrop reaction coordinate it should matter.

Greetings
Thomas

Am 17.02.2012 17:07, schrieb gmx-users-requ...@gromacs.org:

Hi Thomas Many thanks for the reply again. At larger distances the two
curves match up quite well. The curve from the reversible work theorem
is better behaved and smoother but this could be solely due to
statistics. I am slightly confused about your statement "If the small
circle moves between 0 and any value <0 everything should be fine." Do
you not mean 0 and any value >0 ? Cheers Gavin Thomas Schlesier wrote:

>  Hi Gavin,
>  if i remember correctly it was a system about pulling a ligand from a
>  binding pocket?
>  To make the system simpler we have a big circle and in the middle a
>  small circle. And we assume that the potential minimum for the
>  interaction between both circles is when the small cirlce is in the
>  middle of the large circle.
>  Now we do the Umbrella sampling. For a window which is centered at a
>  distance which is sligthly greater then 0, we will get problems.
>  Assume small circle is sligthly shifted to the right. And the other
>  windows are also in this dircetion. (->  reaction coordinate goes from
>  zero to the right dircetion)
>  If the small circle moves between 0 and any value<0 everythig should
>  be fine. But if the small circle moves to the left, we will also get a
>  positive distance. Problem is from the above defined reaction
>  coordinate it should be a negative distance. So we are counting the
>  positive distances too much.
>  To check this, you could use*g_dist*  to calculate the distance for
>  both molecules for the problematic windows. Then project the resulting
>  vector onto your reaction coordinate. Then you should see the
>  crossings between the right and left side.
>
>  How do the two free energy curves compare for larger distances, where
>  you can be sure, that you do not have this 'crossing problem'?
>
>  Greetings
>  Thomas
>
>
>
>  
-
>
>
>
>  Hi all
>
>  I am returning to a query I had a few weeks ago regarding a discrepancy
>  between two free energy curves. One calculated using umbrella sampling,
>  the other calculated via the reversible work theorem from the RDF. There
>  is sufficient sampling of the dynamics in the RDF so this method is
>  viable.
>  Anyway in the pull-code I use pull_geometry = dist and pull_dim=Y Y Y.
>  The free energy curve from the pull-code method does not give me a
>  minimum at the zero value of the order parameter whereas the RDF method
>  does. Someone said before about double counting of positive distances at
>  small values of the order parameter and therefore information is lost at
>  very small distances.
>
>  Is this correct?
>  I am slightly concerned that my curves are not giving me the correct
>  information involving a very important state in my reaction coordinate.
>
>  Also when this dist restraint (which cannot be negative) is implemented
>  are there issues with the normalisation of the histograms from g_wham?
>
>  Cheers
>
>  Gavin

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Re: [gmx-users] pull-code

Hi Thomas

I am sorry to bother you but if you could answer a few questions I have
about how the pull-code works with respect to my system I would really
appreciate it.
My system is a liquid and I am trying to pull one substituent of one
liquid molecule in a certain region of another liquid molecule using as
I said earlier pull_geometry =dist and pull_dim =YYY.
Also pull_start = no
Say I have a window with pull_init=0

1) At the very start of the simulation the pullcode calculates the
vector between the two groups? Is there anything particularly
significant about this initial vector? Is this distance vector
recalculated at every step?
2) Does it compare the distance vector an time t with that at time 0.?
3) Given the initial vector can this vector change (i.e. dierection) or
does the distance between the two groups vary only along this vector
(i.e. in a line) ?

Cheers

Gavin


Thomas Schlesier wrote:
> Hi Gavin,
> if i remember correctly it was a system about pulling a ligand from a
> binding pocket?
> To make the system simpler we have a big circle and in the middle a
> small circle. And we assume that the potential minimum for the
> interaction between both circles is when the small cirlce is in the
> middle of the large circle.
> Now we do the Umbrella sampling. For a window which is centered at a
> distance which is sligthly greater then 0, we will get problems.
> Assume small circle is sligthly shifted to the right. And the other
> windows are also in this dircetion. (-> reaction coordinate goes from
> zero to the right dircetion)
> If the small circle moves between 0 and any value <0 everythig should
> be fine. But if the small circle moves to the left, we will also get a
> positive distance. Problem is from the above defined reaction
> coordinate it should be a negative distance. So we are counting the
> positive distances too much.
> To check this, you could use *g_dist* to calculate the distance for
> both molecules for the problematic windows. Then project the resulting
> vector onto your reaction coordinate. Then you should see the
> crossings between the right and left side.
>
> How do the two free energy curves compare for larger distances, where
> you can be sure, that you do not have this 'crossing problem'?
>
> Greetings
> Thomas
>
>
>
> -
>
>
>
> Hi all
>
> I am returning to a query I had a few weeks ago regarding a discrepancy
> between two free energy curves. One calculated using umbrella sampling,
> the other calculated via the reversible work theorem from the RDF. There
> is sufficient sampling of the dynamics in the RDF so this method is
> viable.
> Anyway in the pull-code I use pull_geometry = dist and pull_dim=Y Y Y.
> The free energy curve from the pull-code method does not give me a
> minimum at the zero value of the order parameter whereas the RDF method
> does. Someone said before about double counting of positive distances at
> small values of the order parameter and therefore information is lost at
> very small distances.
>
> Is this correct?
> I am slightly concerned that my curves are not giving me the correct
> information involving a very important state in my reaction coordinate.
>
> Also when this dist restraint (which cannot be negative) is implemented
> are there issues with the normalisation of the histograms from g_wham?
>
> Cheers
>
> Gavin
>
>

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Re: [gmx-users] pull-code

Hi Thomas

Many thanks for the reply again. At larger distances the two curves
match up quite well. The curve from the reversible work theorem is
better behaved and smoother but this could be solely due to statistics.
I am slightly confused about your statement
"If the small circle moves between 0 and any value <0 everything should
be fine."
Do you not mean 0 and any value >0 ?

Cheers

Gavin

Thomas Schlesier wrote:
> Hi Gavin,
> if i remember correctly it was a system about pulling a ligand from a
> binding pocket?
> To make the system simpler we have a big circle and in the middle a
> small circle. And we assume that the potential minimum for the
> interaction between both circles is when the small cirlce is in the
> middle of the large circle.
> Now we do the Umbrella sampling. For a window which is centered at a
> distance which is sligthly greater then 0, we will get problems.
> Assume small circle is sligthly shifted to the right. And the other
> windows are also in this dircetion. (-> reaction coordinate goes from
> zero to the right dircetion)
> If the small circle moves between 0 and any value <0 everythig should
> be fine. But if the small circle moves to the left, we will also get a
> positive distance. Problem is from the above defined reaction
> coordinate it should be a negative distance. So we are counting the
> positive distances too much.
> To check this, you could use *g_dist* to calculate the distance for
> both molecules for the problematic windows. Then project the resulting
> vector onto your reaction coordinate. Then you should see the
> crossings between the right and left side.
>
> How do the two free energy curves compare for larger distances, where
> you can be sure, that you do not have this 'crossing problem'?
>
> Greetings
> Thomas
>
>
>
> -
>
>
>
> Hi all
>
> I am returning to a query I had a few weeks ago regarding a discrepancy
> between two free energy curves. One calculated using umbrella sampling,
> the other calculated via the reversible work theorem from the RDF. There
> is sufficient sampling of the dynamics in the RDF so this method is
> viable.
> Anyway in the pull-code I use pull_geometry = dist and pull_dim=Y Y Y.
> The free energy curve from the pull-code method does not give me a
> minimum at the zero value of the order parameter whereas the RDF method
> does. Someone said before about double counting of positive distances at
> small values of the order parameter and therefore information is lost at
> very small distances.
>
> Is this correct?
> I am slightly concerned that my curves are not giving me the correct
> information involving a very important state in my reaction coordinate.
>
> Also when this dist restraint (which cannot be negative) is implemented
> are there issues with the normalisation of the histograms from g_wham?
>
> Cheers
>
> Gavin
>
>

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[gmx-users] pull-code


Hi Gavin,
if i remember correctly it was a system about pulling a ligand from a 
binding pocket?
To make the system simpler we have a big circle and in the middle a 
small circle. And we assume that the potential minimum for the 
interaction between both circles is when the small cirlce is in the 
middle of the large circle.
Now we do the Umbrella sampling. For a window which is centered at a 
distance which is sligthly greater then 0, we will get problems. Assume 
small circle is sligthly shifted to the right. And the other windows are 
also in this dircetion. (-> reaction coordinate goes from zero to the 
right dircetion)
If the small circle moves between 0 and any value <0 everythig should be 
fine. But if the small circle moves to the left, we will also get a 
positive distance. Problem is from the above defined reaction coordinate 
it should be a negative distance. So we are counting the positive 
distances too much.
To check this, you could use *g_dist* to calculate the distance for both 
molecules for the problematic windows. Then project the resulting vector 
onto your reaction coordinate. Then you should see the crossings between 
the right and left side.


How do the two free energy curves compare for larger distances, where 
you can be sure, that you do not have this 'crossing problem'?


Greetings
Thomas



-


Hi all

I am returning to a query I had a few weeks ago regarding a discrepancy
between two free energy curves. One calculated using umbrella sampling,
the other calculated via the reversible work theorem from the RDF. There
is sufficient sampling of the dynamics in the RDF so this method is viable.
Anyway in the pull-code I use pull_geometry = dist and pull_dim=Y Y Y.
The free energy curve from the pull-code method does not give me a
minimum at the zero value of the order parameter whereas the RDF method
does. Someone said before about double counting of positive distances at
small values of the order parameter and therefore information is lost at
very small distances.

Is this correct?
I am slightly concerned that my curves are not giving me the correct
information involving a very important state in my reaction coordinate.

Also when this dist restraint (which cannot be negative) is implemented
are there issues with the normalisation of the histograms from g_wham?

Cheers

Gavin


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[gmx-users] pull-code

Hi all

I am returning to a query I had a few weeks ago regarding a discrepancy
between two free energy curves. One calculated using umbrella sampling, 
the other calculated via the reversible work theorem from the RDF. There
is sufficient sampling of the dynamics in the RDF so this method is viable.
Anyway in the pull-code I use pull_geometry = dist and pull_dim=Y Y Y.
The free energy curve from the pull-code method does not give me a
minimum at the zero value of the order parameter whereas the RDF method
does. Someone said before about double counting of positive distances at
small values of the order parameter and therefore information is lost at
very small distances.

Is this correct?
I am slightly concerned that my curves are not giving me the correct
information involving a very important state in my reaction coordinate.

Also when this dist restraint (which cannot be negative) is implemented
are there issues with the normalisation of the histograms from g_wham?

Cheers

Gavin
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[gmx-users] Pull code problem: Large fluctuations in pull force in Gromacs 4.5.1 compared to 4.0.5

2012-01-12 Thread Emma Eriksson

Dear all,
I have a problem using the pull code in Gromacs 4.5.1. I am running simulations 
with a small molecule at constrained distances from the bilayer center in a 
membrane (z-direction) in order to calculate permeability data. I use the force 
acting on the molecule (pullf.xvg) at different distances to calculate free 
energy profiles and diffusion coefficients.
The problem I am facing is that the pull forces are fluctuating significantly 
more in version 4.5.1 compared to in 4.0.5. In 4.0.5 the forces normally 
fluctuate in the range of at most ±2000 kJ/mol/nm whereas in 4.5.1 they 
fluctuate in the range of at most ±5 kJ/mol/nm. The average force is 
however similar in both versions, which results in reasonable calculated free 
energy profiles. However, the large fluctuations in forces make the 
autocorrelation function of the force different, and this causes problems when 
calculating diffusion coefficients.
I have used the same mdp file as in version 4.0.5 with the difference that 
tau_t is increased from 0.1 to 0.4 (mdp file included below). The simulations 
are at least 7 ns. Is there anything trivial that I have missed when changing 
from version 4.0.5 to 4.5.1?
I would really appreciate any help on this issue. Thanks in advance.

Regards,
Emma


The mdp file:

title= x
cpp = /lib/cpp
include   =
define =
integrator= md
dt= 0.002
nsteps   = 750
nstlog= 25000
nstenergy= 30
nstxout= 0
nstxtcout = 25000
nstvout= 0
nstfout = 0
xtc_grps   = DPPC SOL X
energygrps  = DPPC SOL X
nstlist= 10
ns_type   = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype  = Cut-off
rvdw = 1.0
tcoupl   = Nose-hoover
tc-grps  = DPPC SOL X
tau_t= 0.4 0.4 0.4
ref_t  = 323 323 323
Pcoupl  = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p= 1.0 1.0
compressibility  = 4.5e-5 4.5e-5
ref_p= 1.0 1.0
gen_vel= yes
gen_temp   = 323
gen_seed= 173529
constraints  = all-bonds

pbc = xyz

optimize_fft   = yes
unconstrained_start  = no

pull = constraint
pull_geometry  = cylinder
pull_r1  = 1.0
pull_r0  = 1.5
pull_group0= DPPC
pull_group1= X
pull_vec1 = 0 0 1
pull_init1 = -0.006
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Re: [gmx-users] pull code problem: between protofilaments

2011-10-03 Thread Shilpi Chaurasia

Dear Chris,

Thank a lot for your reply. I am trying the pull code that you have suggested. 
And I would be more specific about the problem and code in my future mails.

regards,
Shilpi 

On 02/10/11, chris.ne...@utoronto.ca wrote:
> Dear Shilpi:
> 
> Can you use something like this?
> 
> pull = umbrella
> pull_geometry    = position
> pull_dim = N N Y
> pull_vec1    = 0 0 0
> pull_start   = no
> pull_ngroups = 1
> pull_group0  = PRO-1
> pull_pbcatom0    = 
> pull_group1  = PRO-2
> pull_pbcatom1    = 
> pull_init1   = 0 0 
> pull_rate1   = 0
> pull_k1  = 500.0
> pull_nstxout = 500
> pull_nstfout = 500
> 
> The above is for umbrella sampling. If you want to do continuous pulling, 
> then:
> 
> pull_start   = yes
> pull_rate1   = 
> 
> ### Also:
> 
> Next time you post, please provide more specifics. For example, I suggested a 
> .mdp file in specifics to you above and I bet it would have been harder for 
> you to guess what I meant if I had just told you the general idea instead of 
> pasting some .mdp options. Likewise, your initial post would have been 
> clearer it you had copied and pasted the .mdp pull code section that you 
> tried to use.
> 
> Chris.
> 
> -- original message --
> 
> 
> Dear Gmx users,
> 
> I am
> studying the interaction between the tubulin protofilaments arranged
>  in parallel. For this operation, I have considered a tetramer and a dimer 
> from two protofilaments
> respectively (say PRO-1 and PRO-2), tetramer in PRO-1 and a dimer in
> PRO-2. I want to
>  move the dimer of PRO-2 over the tetramer of PRO-1 along the length of
> protofilaments in one axis only, keeping the PRO-1 fixed to its original
> position. I tried by assuming tetramer as 'reference group' and the
> dimer as 'pull group' in pull code but the system crashed.
> 
> I have
> succeeded in separating two dimers in Z-axis by using
> 'distance' geometry. But this case is quite different, as the pulling is
>  not face-to-face but rather a sliding movement over another
> protofilament. Here, the COM distance between the pull group (dimer of
> PRO-2) and reference group (tetramer of PRO-1) first decreases and then 
> increases while it moves. How can I simulate this operation by using pull 
> code?
> 
> Thanks,
> 
> best regards,
> Shilpi Chaurasia
> 
> 
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[gmx-users] pull code problem: between protofilaments

2011-10-02 Thread chris . neale


Dear Shilpi:

Can you use something like this?

pull = umbrella
pull_geometry= position
pull_dim = N N Y
pull_vec1= 0 0 0
pull_start   = no
pull_ngroups = 1
pull_group0  = PRO-1
pull_pbcatom0= 
pull_group1  = PRO-2
pull_pbcatom1= 
pull_init1   = 0 0 
pull_rate1   = 0
pull_k1  = 500.0
pull_nstxout = 500
pull_nstfout = 500

The above is for umbrella sampling. If you want to do continuous  
pulling, then:


pull_start   = yes
pull_rate1   = 

### Also:

Next time you post, please provide more specifics. For example, I  
suggested a .mdp file in specifics to you above and I bet it would  
have been harder for you to guess what I meant if I had just told you  
the general idea instead of pasting some .mdp options. Likewise, your  
initial post would have been clearer it you had copied and pasted the  
.mdp pull code section that you tried to use.


Chris.

-- original message --


Dear Gmx users,

I am
studying the interaction between the tubulin protofilaments arranged
 in parallel. For this operation, I have considered a tetramer and a  
dimer from two protofilaments

respectively (say PRO-1 and PRO-2), tetramer in PRO-1 and a dimer in
PRO-2. I want to
 move the dimer of PRO-2 over the tetramer of PRO-1 along the length of
protofilaments in one axis only, keeping the PRO-1 fixed to its original
position. I tried by assuming tetramer as 'reference group' and the
dimer as 'pull group' in pull code but the system crashed.

I have
succeeded in separating two dimers in Z-axis by using
'distance' geometry. But this case is quite different, as the pulling is
 not face-to-face but rather a sliding movement over another
protofilament. Here, the COM distance between the pull group (dimer of
PRO-2) and reference group (tetramer of PRO-1) first decreases and  
then increases while it moves. How can I simulate this operation by  
using pull code?


Thanks,

best regards,
Shilpi Chaurasia


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[gmx-users] pull code problem: between protofilaments

2011-09-29 Thread Shilpi Chaurasia

Dear Gmx users,

I am 
studying the interaction between the tubulin protofilaments arranged
 in parallel. For this operation, I have considered a tetramer and a dimer from 
two protofilaments 
respectively (say PRO-1 and PRO-2), tetramer in PRO-1 and a dimer in 
PRO-2. I want to
 move the dimer of PRO-2 over the tetramer of PRO-1 along the length of 
protofilaments in one axis only, keeping the PRO-1 fixed to its original 
position. I tried by assuming tetramer as 'reference group' and the 
dimer as 'pull group' in pull code but the system crashed. 

I have 
succeeded in separating two dimers in Z-axis by using 
'distance' geometry. But this case is quite different, as the pulling is
 not face-to-face but rather a sliding movement over another 
protofilament. Here, the COM distance between the pull group (dimer of 
PRO-2) and reference group (tetramer of PRO-1) first decreases and then 
increases while it moves. How can I simulate this operation by using pull 
code?  

Thanks,

best regards,
Shilpi Chaurasia
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Re: [gmx-users] pull code: distance between pull grp and ref grp is more than usual at the begining of simulation (at 1st time frame 1 ps)

2011-09-13 Thread Justin A. Lemkul




Shilpi Chaurasia wrote:

Dear Justin,

Thanks a lot for your reply.
Here I am providing the data and explaining the problem in detail:

I hope that it will help you in understanding in a better way. 
Considering the tetramer as 'abcd'.  'ab' as one dimer and 'cd' as 
another, I want to separate 'ab' and 'cd'. Length of each dimer is 8 nm, 
so the tetramer (initial configuration) is approximately 16 nm and I 
have used a cubic box of 30 nm. Two groups (reference group and pull 
group) are decided on the basis of residue numbers forming 'ab' as 
reference grp and 'bc' as pull group by making an index file.




I will assume you mean CD here.  If your groups are AB and BC, then you'll 
certainly have problems.


I have verified that the initial configuration does not split across 
periodic boundaries, it is always inside the box throughout the 
simulation. Moreover, the initial distance is not equal to box vector.


By g_dist , I have tried to calculate the distance between the two 
groups and it came out to be approx. 15 nm (Please have a look at the 
dist.xvg file at the end). Do you think that in the first ps time frame, 
should it get separated by 15 nm?? Please correct me if I have done 
anything wrong.




If the dimer truly is together, then I would think this distance is too large 
unless (1) it actually is actually split across PBC, (2) your size calculations 
are wrong, or (3) your index groups are wrong.  In any case, I can see this 
being a problem.  A distance of 15 nm is 50% of the box size, and as soon as 
separation occurs, your pulling reference distance will be greater than 50% of 
the box vector, which causes a periodic distance to be calculated.  Either use 
the distance_periodic pulling geometry or use a larger box.


See below for a few thoughts on the dist.xvg data.

By mistake, in my last mail I wrote that I need to pull along Y axis. In 
actual, it is Z-axis and I have used pull_dim N N Y. So it is just the 
mistake in writing the mail.


Please let me know do you need any other data or parameters that I have 
used during this simulation.


It would also be useful to know what grompp printed as the reference distance at 
time t=0.


Here's why I think periodicity is indeed an issue:


   0.000   15.0342455   -0.7714367   -0.9718266   14.9829559
   0.500   15.0345469   -0.7726345   -0.9766102  -14.9828863


Note that within 0.5 ps, the sign of the z-distance has changed but the 
magnitude is basically the same.  This indicates to me that your dimer is 
dancing back and forth across a periodic boundary.  The output of pullx.xvg 
would also be informative to confirm this phenomenon.


-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] pull code: distance between pull grp and ref grp is more than usual at the begining of simulation (at 1st time frame 1 ps)

2011-09-13 Thread Shilpi Chaurasia

Dear Justin,



Thanks a lot for your reply.

Here I am providing the data and explaining the problem in detail:



I hope that it will help you in understanding in a better way. 
Considering the tetramer as 'abcd'.  'ab' as one dimer and 'cd' as 
another, I want to separate 'ab' and 'cd'. Length of each dimer is 8 nm,
 so the tetramer (initial configuration) is approximately 16 nm and I 
have used a cubic box of 30 nm. Two groups (reference group and pull 
group) are decided on the basis of residue numbers forming 'ab' as 
reference grp and 'bc' as pull group by making an index file. 



I have verified that the initial configuration does not split across 
periodic boundaries, it is always inside the box throughout the 
simulation. Moreover, the initial distance is not equal to box vector. 



By g_dist , I have tried to calculate the distance between the two groups and 
it came out to be approx. 15 nm (Please have a look at the dist.xvg
 file at the end). Do you think that in the first ps time frame, should 
it get separated by 15 nm?? Please correct me if I have done anything 
wrong.



By mistake, in my last mail I wrote that I need to pull along Y axis. In
 actual, it is Z-axis and I have used pull_dim N N Y. So it is just the 
mistake in writing the mail.



Please let me know do you need any other data or parameters that I have used 
during this simulation.

An early reply would me much appreciated.





---

---

dist.xvg





# This file was created Tue Sep 13 11:09:23 2011

# by the following command:

# g_dist -f tub_pull.xtc -s tub_pull.tpr -n index.ndx 

#

# g_dist is part of G R O M A C S:

#

# Giving Russians Opium May Alter Current Situation

#

@    title "Distance"

@    xaxis  label "Time (ps)"

@    yaxis  label "Distance (nm)"

@TYPE xy

@ view 0.15, 0.15, 0.75, 0.85

@ legend on

@ legend box on

@ legend loctype view

@ legend 0.78, 0.8

@ legend length 2

@ s0 legend "|d|"

@ s1 legend "d\sx\N"

@ s2 legend "d\sy\N"

@ s3 legend "d\sz\N"

   0.000   15.0342455   -0.7714367   -0.9718266   14.9829559

   0.500   15.0345469   -0.7726345   -0.9766102  -14.9828863

   1.000   15.0345631   -0.7665710   -0.9862967  -14.9825792

   1.500   15.0343399   -0.7575226   -0.9916229   14.9824638

   2.000   15.0335970   -0.7490749   -0.9957008  -14.9818726

   2.500   15.0322971   -0.7446661   -0.9996347  -14.9805260

   3.000   15.0341187   -0.7364883   -1.0029345  -14.9825373

   3.500   15.0331717   -0.7328205   -1.0078001   14.9814405

   4.000   15.0311899   -0.7334194   -1.0118599   14.9791489

   4.500   15.0334759   -0.7351160   -1.0128736   14.9812908

   5.000   15.0336533   -0.7327585   -1.0102243   14.9817638

   5.500   15.0327044   -0.7342167   -1.0076447   14.9809132

   6.000   15.0335188   -0.7365904   -1.0090990  -14.9815168

   6.500   15.0296631   -0.7375288   -1.0111809  -14.9774609

   7.000   15.0294476   -0.7318525   -1.0155020  -14.9772310

   7.500   15.0322533   -0.7323456   -1.0173597  -14.9798965

   8.000   15.0353861   -0.7333517   -1.0172930   14.9829950

   8.500   15.0323915   -0.7285290   -1.0122719   14.9805660

   9.000   15.0284719   -0.7241497   -1.0072327   14.9771843

   9.500   15.0285101   -0.7232113   -1.0051012   14.9774113

  10.000   15.0306396   -0.7257242   -1.0020084   14.9796333

  10.500   15.0324621   -0.7242069   -0.9959688   14.9819384

  11.000   15.0324860   -0.7183657   -0.9881392  -14.9827623

  11.500   15.0308609   -0.7121477   -0.9848318  -14.9816465

  12.000   15.0318832   -0.7091122   -0.9842033   14.9828577

  12.500   15.0316772   -0.7063818   -0.9834919  -14.9828262

  13.000   15.0291939   -0.7024584   -0.9846754  -14.9804420

  13.500   15.0307999   -0.7052488   -0.9864941   14.9818020

  14.000   15.0286407   -0.7049980   -0.9902172   14.9794016

  14.500   15.0301456   -0.7010813   -0.9916439  -14.9810019

  15.000   15.0305882   -0.6967783   -0.9922857  -14.9816036

  15.500   15.0319242   -0.6941795   -0.9950562   14.9828815

  16.000   15.0315027   -0.6892128   -0.9928131   14.9828358

  16.500   15.0314274   -0.6889334   -0.9883585  -14.9830685

  17.000   15.0296593   -0.6906672   -0.9852924   14.9814167

  17.500   15.0277662   -0.6964712   -0.9844646  -14.9793034

  18.000   15.03

Re: [gmx-users] pull code: distance between pull grp and ref grp is more than usual at the begining of simulation (at 1st time frame 1 ps)

2011-09-09 Thread Justin A. Lemkul




Shilpi Chaurasia wrote:
 I am trying to pull apart two dimers of tubulin protein joined 
together, to form two separate dimers by steered molecular dynamics 
using Pull code. The objective is to separate the dimers by pulling 
along one axis only (Y axis). I ran the simulation for 25 ps and it 
accomplished well but while visualizing the trajectory in VMD, in the 
very beginning (first frame), dimers are at distance which is much 
greater than expected. I expected that in first frame they should not 
have separated too much (i.e. in just 1 ps, they are at greater 
distance) I guess this is unusual. Please let me know where I am doing 
wrong? I have used the following pull code:




Actual numbers would help.  Is your initial configuration simply split across 
periodic boundaries?  If the initial distance is roughly equivalent to one of 
the box vectors, then that's the case.  Otherwise, please provide real data and 
check to make sure your pull groups are what you think they are.



pull= umbrella
pull_geometry   = distance
pull_dim= N N Y


Note that you're not actually pulling along Y as you state above.  Here, you're 
pulling along Z.  Perhaps that's one issue.


-Justin

pull_start  = yes 
pull_init1  = 0.0

pull_ngroups= 1
pull_group0 = dimer_ref   ; reference group (based on 
index file)

pull_group1 = dimer_pull   ; pull group
pull_rate1  = 0.1  
pull_k1 = 1000 
pull_nstfout= 10  
pull_nstxout= 10


best regards,
Shilpi Chaurasia



--


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] pull code: distance between pull grp and ref grp is more than usual at the begining of simulation (at 1st time frame 1 ps)

2011-09-09 Thread Shilpi Chaurasia

 I am trying to pull apart two dimers of tubulin protein joined together, to 
form two separate dimers by steered molecular dynamics using Pull code. The 
objective is to separate the dimers by pulling along one axis only (Y axis). I 
ran the simulation for 25 ps and it accomplished well but while visualizing the 
trajectory in VMD, in the very beginning (first frame), dimers are at distance 
which is much greater than expected. I expected that in first frame they should 
not have separated too much (i.e. in just 1 ps, they are at greater distance) I 
guess this is unusual. Please let me know where I am doing wrong? I have used 
the following pull code:

pull    = umbrella
pull_geometry   = distance
pull_dim    = N N Y
pull_start  = yes  
pull_init1  = 0.0
pull_ngroups    = 1
pull_group0 = dimer_ref   ; reference group (based on index 
file)
pull_group1 = dimer_pull   ; pull group
pull_rate1  = 0.1   
pull_k1 = 1000  
pull_nstfout    = 10   
pull_nstxout    = 10

best regards,
Shilpi Chaurasia
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Re: [gmx-users] pull code

2011-02-14 Thread Justin A. Lemkul




Poojari, Chetan wrote:

Hi Justin,

As discussed earlier, I removed the restraints from lipids and used constraint 
force for pulling, I was able to pull the peptide to the lower leaf headgroups 
starting from 1.3nm above the upper leaf headgroups. Below is the pull code 
inputs i used:

; Pull code
pull= constraint
pull_geometry   = direction
pull_dim= N N Y
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = POPC
pull_group1 = Protein
pull_vec1   = 0.0 0.0 -1.0
pull_rate1  = 0.013 ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000  ; kJ mol^-1 nm^-2



But going through the summary_distances.dat file i wasnt sure of the 
progression of COM distance between peptide and bilayer.

The first conf.gro starts at 3.84685nm it goes on reducing till it reaches conf 
322  1.0903 nm, at this point when i viewed the 322.gro file the 
peptide is approximately in center of the bilayer. From this point onwards 
distance keeps increasing and it reaches conf 500 at 2.864 nm. But viewing the 
gro. file in vmd from conf 328.. conf 500, the peptide is being pulled to 
the lower leaf headgroups.   So the peptide was pulled to the lower leaf 
headgroup as expected but I am not sure with the progression.

0   3.8468513
1   3.8324797
2   3.8197916
.
.
.
322  1.0903752
.
.
328 1.1572036
.
.
498 2.8465521
499 2.8731604
500 2.8649662



From here i carried on to do umbrella simulations for 24 windows which i 
generated for 10ns each, below is the pull code which  i used for umbrella 
samplingafter analysis PMF converges and looking at the histogram 
theres sufficient overlap between windows. But due to increase in progression 
after conf 322 till conf 500 some peaks in the histogram looks like written 
twice.


; Pull code
pull= umbrella
pull_geometry   = distance
pull_dim= N N Y
pull_start  = yes
pull_ngroups= 1
pull_group0 = POPC
pull_group1 = Protein
pull_init1  = 0
pull_rate1  = 0.0
pull_k1 = 1000  ; kJ mol^-1 nm^-2
pull_nstxout= 1000  ; every 2 ps
pull_nstfout= 1000  ; every 2 ps




You've got a scenario for which the tutorial's input files will not suffice for 
your purposes.  The simple example in the tutorial is for a linear pull 
resulting in a continually increasing COM distance.  In your case, you are 
starting at a relative positive COM displacement, and ending at a negative one 
(i.e., below the POPC COM).  For this application, you'll need to use a 
different pull_geometry (probably "position"), and perhaps other options.  There 
are examples in the list archive, if you spend some time searching.


-Justin




Kind regards,
chetan



From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 10 February 2011 12:33
To: Gromacs Users' List
Subject: Re: [gmx-users] pull code

Poojari, Chetan wrote:

Hi Justin,

Thank you very much for your suggestions. I will use constraint force  to
force a peptide into a membrane with pulling for longer time.

yes with "POSRES_LIPID"   i am keeping the lipids rigid while pulling the
peptide inside.  Should the lipids be flexible while pulling??



If your lipids are completely rigid, then they will not be happy accommodating
the introduction of a peptide into that environment.


I am using pull_geometry   = direction, In the tutorial mdp file you had
commented saying cant get PMF with direction. So please can I know if this
error of not getting PMF with direction fixed or with pull_geometry   =
distance will i be able to pull the peptide into membrane with still using
pull direction pull_vec1   = 0.0 0.0 -1.0



You're not doing umbrella sampling, you're doing steered MD, which is a
non-equilibrium process.  Please read the tutorial carefully.

-Justin




Kind regards, chetan


 From: gmx-users-boun...@gromacs.org
[gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul
[jalem...@vt.edu] Sent: 09 February 2011 16:40 To: Discussion list for
GROMACS users Subject: Re: [gmx-users] pull code

Poojari, Chetan wrote:

Hi,

I am using umbrella sampling to pull my peptide (peptide starting from
above the lipid bilayer) into the hydrophobic core of the lipid bilayer.

Following are my inputs i have used:

title   = Umbrella pulling simulation define  =
-DPOSRES_LIPID ; Run parameters integrator  = md dt  =
0.002 tinit   = 0 nsteps  = 25; 500 ps nstcomm
= 1 . . ; Pull code pull= umbrella pull_geometry   = direction
pull_dim= N N Y pull_start  = yes   ; define initial
COM distance > 0 pull_ngroups= 1 pull_group0 = POPC pull_group1
= Prote

RE: [gmx-users] pull code

2011-02-14 Thread Poojari, Chetan

Hi Justin,

As discussed earlier, I removed the restraints from lipids and used constraint 
force for pulling, I was able to pull the peptide to the lower leaf headgroups 
starting from 1.3nm above the upper leaf headgroups. Below is the pull code 
inputs i used:

; Pull code
pull= constraint
pull_geometry   = direction
pull_dim= N N Y
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = POPC
pull_group1 = Protein
pull_vec1   = 0.0 0.0 -1.0
pull_rate1  = 0.013 ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000  ; kJ mol^-1 nm^-2

But going through the summary_distances.dat file i wasnt sure of the 
progression of COM distance between peptide and bilayer.

The first conf.gro starts at 3.84685nm it goes on reducing till it reaches conf 
322  1.0903 nm, at this point when i viewed the 322.gro file the 
peptide is approximately in center of the bilayer. From this point onwards 
distance keeps increasing and it reaches conf 500 at 2.864 nm. But viewing the 
gro. file in vmd from conf 328.. conf 500, the peptide is being pulled to 
the lower leaf headgroups.   So the peptide was pulled to the lower leaf 
headgroup as expected but I am not sure with the progression.

0   3.8468513
1   3.8324797
2   3.8197916
.
.
.
322  1.0903752
.
.
328 1.1572036
.
.
498 2.8465521
499 2.8731604
500 2.8649662

>From here i carried on to do umbrella simulations for 24 windows which i 
>generated for 10ns each, below is the pull code which  i used for umbrella 
>samplingafter analysis PMF converges and looking at the histogram 
>theres sufficient overlap between windows. But due to increase in progression 
>after conf 322 till conf 500 some peaks in the histogram looks like written 
>twice.

; Pull code
pull= umbrella
pull_geometry   = distance
pull_dim= N N Y
pull_start  = yes
pull_ngroups= 1
pull_group0 = POPC
pull_group1 = Protein
pull_init1  = 0
pull_rate1  = 0.0
pull_k1 = 1000  ; kJ mol^-1 nm^-2
pull_nstxout= 1000  ; every 2 ps
pull_nstfout= 1000  ; every 2 ps

Kind regards,
chetan

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 10 February 2011 12:33
To: Gromacs Users' List
Subject: Re: [gmx-users] pull code

Poojari, Chetan wrote:
> Hi Justin,
>
> Thank you very much for your suggestions. I will use constraint force  to
> force a peptide into a membrane with pulling for longer time.
>
> yes with "POSRES_LIPID"   i am keeping the lipids rigid while pulling the
> peptide inside.  Should the lipids be flexible while pulling??
>

If your lipids are completely rigid, then they will not be happy accommodating
the introduction of a peptide into that environment.

> I am using pull_geometry   = direction, In the tutorial mdp file you had
> commented saying cant get PMF with direction. So please can I know if this
> error of not getting PMF with direction fixed or with pull_geometry   =
> distance will i be able to pull the peptide into membrane with still using
> pull direction pull_vec1   = 0.0 0.0 -1.0
>

You're not doing umbrella sampling, you're doing steered MD, which is a
non-equilibrium process.  Please read the tutorial carefully.

-Justin

>
>
>
> Kind regards, chetan
>
>
>  From: gmx-users-boun...@gromacs.org
> [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul
> [jalem...@vt.edu] Sent: 09 February 2011 16:40 To: Discussion list for
> GROMACS users Subject: Re: [gmx-users] pull code
>
> Poojari, Chetan wrote:
>> Hi,
>>
>> I am using umbrella sampling to pull my peptide (peptide starting from
>> above the lipid bilayer) into the hydrophobic core of the lipid bilayer.
>>
>> Following are my inputs i have used:
>>
>> title   = Umbrella pulling simulation define  =
>> -DPOSRES_LIPID ; Run parameters integrator  = md dt  =
>> 0.002 tinit   = 0 nsteps  = 25; 500 ps nstcomm
>> = 1 . . ; Pull code pull= umbrella pull_geometry   = direction
>> pull_dim= N N Y pull_start  = yes   ; define initial
>> COM distance > 0 pull_ngroups= 1 pull_group0 = POPC pull_group1
>> = Protein pull_vec1   = 0.0 0.0 -1.0 pull_rate1  = 0.01  ;
>> 0.01 nm per ps = 10 nm per ns pull_k1 = 1000  ; kJ mol^-1
>> nm^-2
>>
>>
>> After running the this step:  grompp -f md_pull.mdp -c npt.gro -p topol.top
>> -n index.ndx -t npt.cpt -o pull.tpr
>>
>> i get grompp ou

Re: [gmx-users] pull code

2011-02-10 Thread Justin A. Lemkul




Poojari, Chetan wrote:

Hi Justin,

Thank you very much for your suggestions. I will use constraint force  to
force a peptide into a membrane with pulling for longer time.

yes with "POSRES_LIPID"   i am keeping the lipids rigid while pulling the
peptide inside.  Should the lipids be flexible while pulling??



If your lipids are completely rigid, then they will not be happy accommodating 
the introduction of a peptide into that environment.



I am using pull_geometry   = direction, In the tutorial mdp file you had
commented saying cant get PMF with direction. So please can I know if this
error of not getting PMF with direction fixed or with pull_geometry   =
distance will i be able to pull the peptide into membrane with still using
pull direction pull_vec1   = 0.0 0.0 -1.0



You're not doing umbrella sampling, you're doing steered MD, which is a 
non-equilibrium process.  Please read the tutorial carefully.


-Justin





Kind regards, chetan


 From: gmx-users-boun...@gromacs.org
[gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul
[jalem...@vt.edu] Sent: 09 February 2011 16:40 To: Discussion list for
GROMACS users Subject: Re: [gmx-users] pull code

Poojari, Chetan wrote:

Hi,

I am using umbrella sampling to pull my peptide (peptide starting from
above the lipid bilayer) into the hydrophobic core of the lipid bilayer.

Following are my inputs i have used:

title   = Umbrella pulling simulation define  =
-DPOSRES_LIPID ; Run parameters integrator  = md dt  =
0.002 tinit   = 0 nsteps  = 25; 500 ps nstcomm
= 1 . . ; Pull code pull= umbrella pull_geometry   = direction 
pull_dim= N N Y pull_start  = yes   ; define initial

COM distance > 0 pull_ngroups= 1 pull_group0 = POPC pull_group1
= Protein pull_vec1   = 0.0 0.0 -1.0 pull_rate1  = 0.01  ;
0.01 nm per ps = 10 nm per ns pull_k1 = 1000  ; kJ mol^-1
nm^-2


After running the this step:  grompp -f md_pull.mdp -c npt.gro -p topol.top
-n index.ndx -t npt.cpt -o pull.tpr

i get grompp output as such:

Pull group  natoms  pbc atom  distance at start reference at t=0 0
6656  3433 1   10553  -4.132-4.132

I am starting to pull my peptide from 1nm above the upper leaf headgroup. I
am using POPC lipids and distance between 2 adjacent headgroups seem to be
around 4.2 nm.

I want the peptide to be pulled into the bilayer till the lower leaf lipid
headgroups, but the peptide is being pulled only till middle of the
hydrophobic core of the bilayer.

Please can I know what might be the problem ?



Either you're (1) not pulling for sufficient time, (2) not pulling hard
enough, or (3) the physical properties of the system don't allow for such a
position.

For (2), using a harmonic potential to try to force a peptide into a membrane
is probably not a great idea.  A constraint force is probably better.  For
(3), what does "POSRES_LIPID" refer to?  Are you keeping the lipids too rigid
by doing so?


While viewing the conf.*gro file outputed  from the traj. (after extracting
the frames), i found few lipid molecules to be broken. Please can I know if
there is a way to avoid these broken structures??? Is there a possibility
that I am not able to pull the peptide into the lower leaf head group due
to these broken lipid structures?




Please become comfortable with the concept of periodic boundary conditions.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions


-Justin



Any suggestions will be helpful.


Kind regards, chetan.


 


 Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft:
Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B
3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher 
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich

Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr.
Sebastian M. Schmidt 

 





-- 

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 list
gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 
Please search the archive at

http://www.gromacs.org/Support/Mailing_Lists/S

RE: [gmx-users] pull code

2011-02-10 Thread Poojari, Chetan

Hi Justin,

Thank you very much for your suggestions. I will use constraint force  to force 
a peptide into a membrane with pulling for longer time. 

yes with "POSRES_LIPID"   i am keeping the lipids rigid while pulling the 
peptide inside.  Should the lipids be flexible while pulling??

I am using pull_geometry   = direction, In the tutorial mdp file you had 
commented saying cant get PMF with direction. So please can I know if this 
error of not getting PMF with direction fixed or with pull_geometry   = 
distance will i be able to pull the peptide into membrane with still using pull 
direction pull_vec1   = 0.0 0.0 -1.0

Kind regards,
chetan

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 09 February 2011 16:40
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] pull code

Poojari, Chetan wrote:
> Hi,
>
> I am using umbrella sampling to pull my peptide (peptide starting from above 
> the lipid bilayer) into the hydrophobic core of the lipid bilayer.
>
> Following are my inputs i have used:
>
> title   = Umbrella pulling simulation
> define  = -DPOSRES_LIPID
> ; Run parameters
> integrator  = md
> dt  = 0.002
> tinit   = 0
> nsteps  = 25; 500 ps
> nstcomm = 1
> .
> .
> ; Pull code
> pull= umbrella
> pull_geometry   = direction
> pull_dim= N N Y
> pull_start  = yes   ; define initial COM distance > 0
> pull_ngroups= 1
> pull_group0 = POPC
> pull_group1 = Protein
> pull_vec1   = 0.0 0.0 -1.0
> pull_rate1  = 0.01  ; 0.01 nm per ps = 10 nm per ns
> pull_k1 = 1000  ; kJ mol^-1 nm^-2
>
>
> After running the this step:  grompp -f md_pull.mdp -c npt.gro -p topol.top 
> -n index.ndx -t npt.cpt -o pull.tpr
>
> i get grompp output as such:
>
> Pull group  natoms  pbc atom  distance at start reference at t=0
>0  6656  3433
>1   10553  -4.132-4.132
>
> I am starting to pull my peptide from 1nm above the upper leaf headgroup. I 
> am using POPC lipids and distance between 2 adjacent headgroups seem to be 
> around 4.2 nm.
>
> I want the peptide to be pulled into the bilayer till the lower leaf lipid 
> headgroups, but the peptide is being pulled only till middle of the 
> hydrophobic core of the bilayer.
>
> Please can I know what might be the problem ?
>

Either you're (1) not pulling for sufficient time, (2) not pulling hard enough,
or (3) the physical properties of the system don't allow for such a position.

For (2), using a harmonic potential to try to force a peptide into a membrane is
probably not a great idea.  A constraint force is probably better.  For (3),
what does "POSRES_LIPID" refer to?  Are you keeping the lipids too rigid by
doing so?

>
> While viewing the conf.*gro file outputed  from the traj. (after extracting 
> the frames), i found few lipid molecules to be broken. Please can I know if 
> there is a way to avoid these broken structures??? Is there a possibility 
> that I am not able to pull the peptide into the lower leaf head group due to 
> these broken lipid structures?
>
>

Please become comfortable with the concept of periodic boundary conditions.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

>
>
> Any suggestions will be helpful.
>
>
> Kind regards,
> chetan.
>
> 
> 
> Forschungszentrum Juelich GmbH
> 52425 Juelich
> Sitz der Gesellschaft: Juelich
> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
> Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
> Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> Prof. Dr. Sebastian M. Schmidt
> 
> 

--

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
Pl

Re: [gmx-users] pull code

2011-02-09 Thread Justin A. Lemkul




Poojari, Chetan wrote:

Hi,

I am using umbrella sampling to pull my peptide (peptide starting from above 
the lipid bilayer) into the hydrophobic core of the lipid bilayer.

Following are my inputs i have used:

title   = Umbrella pulling simulation
define  = -DPOSRES_LIPID
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 25; 500 ps
nstcomm = 1
.
.
; Pull code
pull= umbrella
pull_geometry   = direction
pull_dim= N N Y
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = POPC
pull_group1 = Protein
pull_vec1   = 0.0 0.0 -1.0
pull_rate1  = 0.01  ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000  ; kJ mol^-1 nm^-2


After running the this step:  grompp -f md_pull.mdp -c npt.gro -p topol.top -n 
index.ndx -t npt.cpt -o pull.tpr

i get grompp output as such:

Pull group  natoms  pbc atom  distance at start reference at t=0
   0  6656  3433
   1   10553  -4.132-4.132

I am starting to pull my peptide from 1nm above the upper leaf headgroup. I am 
using POPC lipids and distance between 2 adjacent headgroups seem to be around 
4.2 nm.

I want the peptide to be pulled into the bilayer till the lower leaf lipid 
headgroups, but the peptide is being pulled only till middle of the hydrophobic 
core of the bilayer.

Please can I know what might be the problem ?



Either you're (1) not pulling for sufficient time, (2) not pulling hard enough, 
or (3) the physical properties of the system don't allow for such a position.


For (2), using a harmonic potential to try to force a peptide into a membrane is 
probably not a great idea.  A constraint force is probably better.  For (3), 
what does "POSRES_LIPID" refer to?  Are you keeping the lipids too rigid by 
doing so?




While viewing the conf.*gro file outputed  from the traj. (after extracting the 
frames), i found few lipid molecules to be broken. Please can I know if there 
is a way to avoid these broken structures??? Is there a possibility that I am 
not able to pull the peptide into the lower leaf head group due to these broken 
lipid structures?




Please become comfortable with the concept of periodic boundary conditions.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin




Any suggestions will be helpful.


Kind regards,
chetan.



Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt




--


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] pull code

2011-02-09 Thread Poojari, Chetan

Hi,

I am using umbrella sampling to pull my peptide (peptide starting from above 
the lipid bilayer) into the hydrophobic core of the lipid bilayer.

Following are my inputs i have used:

title   = Umbrella pulling simulation
define  = -DPOSRES_LIPID
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 25; 500 ps
nstcomm = 1
.
.
; Pull code
pull= umbrella
pull_geometry   = direction
pull_dim= N N Y
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = POPC
pull_group1 = Protein
pull_vec1   = 0.0 0.0 -1.0
pull_rate1  = 0.01  ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000  ; kJ mol^-1 nm^-2


After running the this step:  grompp -f md_pull.mdp -c npt.gro -p topol.top -n 
index.ndx -t npt.cpt -o pull.tpr

i get grompp output as such:

Pull group  natoms  pbc atom  distance at start reference at t=0
   0  6656  3433
   1   10553  -4.132-4.132

I am starting to pull my peptide from 1nm above the upper leaf headgroup. I am 
using POPC lipids and distance between 2 adjacent headgroups seem to be around 
4.2 nm.

I want the peptide to be pulled into the bilayer till the lower leaf lipid 
headgroups, but the peptide is being pulled only till middle of the hydrophobic 
core of the bilayer.

Please can I know what might be the problem ?


While viewing the conf.*gro file outputed  from the traj. (after extracting the 
frames), i found few lipid molecules to be broken. Please can I know if there 
is a way to avoid these broken structures??? Is there a possibility that I am 
not able to pull the peptide into the lower leaf head group due to these broken 
lipid structures?




Any suggestions will be helpful.


Kind regards,
chetan.



Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt


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[gmx-users] Pull code

2011-01-21 Thread Gavin Melaugh

Dear All

Sorry wrong subject title in previous post. Can someone please tell me how to 
generated the plot of mean force
having ran the pull code at several distances using constraints?

Gavin

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[gmx-users] Pull Code for Secondary Stability

2010-09-29 Thread C Johnson


Does anyone know if the pull code can be used to determine structure stability? 
 If I wanted to generate a stress-strain plot of an alpha-helix, would the pull 
simulation give me the data such as the force vs displacement?

Thanks
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Re: [gmx-users] pull code absolute reference

2010-08-18 Thread Justin A. Lemkul




bv07ay wrote:

Hello,
i am having trouble using the pull options in gromacs 4.0.4.  i am 
simply trying to move a protein from the top of the box to a certain 
point in the center.  i have had no luck using a constant pulling or 
umbrella pulling the error i receive is:


"You are using an absolute reference for pulling, but the rest of the
  system does not have an absolute reference. This will lead to artifacts."

here is my most recent .mdp pull options:

; PULL
pull= umbrella
pull_geometry= position
;pull_group0=
pull_init1= 3.279 3.279 3.90
pull_group1= MID
pull_dim= Y Y Y
pull_k1= 50


is there a way to make my system have an absolute reference? or is there 
some other way of pulling it that has worked for others?




The error message is related less to the pull options than it is to COM motion 
removal.  For instance:


http://lists.gromacs.org/pipermail/gmx-users/2009-April/041329.html
http://lists.gromacs.org/pipermail/gmx-users/2006-July/022753.html

If you search the mailing list archives you will find lots of related posts.  I 
pulled those up immediately by searching: "absolute reference" pulling.


-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] pull code absolute reference

2010-08-18 Thread bv07ay


Hello,
i am having trouble using the pull options in gromacs 4.0.4.  i am  
simply trying to move a protein from the top of the box to a certain  
point in the center.  i have had no luck using a constant pulling or  
umbrella pulling the error i receive is:


"You are using an absolute reference for pulling, but the rest of the
  system does not have an absolute reference. This will lead to artifacts."

here is my most recent .mdp pull options:

; PULL
pull= umbrella
pull_geometry= position
;pull_group0=
pull_init1= 3.279 3.279 3.90
pull_group1= MID
pull_dim= Y Y Y
pull_k1= 50


is there a way to make my system have an absolute reference? or is  
there some other way of pulling it that has worked for others?


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[gmx-users] pull code example

2010-07-17 Thread chris . neale


I'd send a list of links except that the other end of a google search for

gromacs pull code example

has all of what you will need to broaden your general pull code  
understanding. The mailing list has an absolutely massive number of  
posts on this too.


Chris.


Hi all,

Could anybody please share some working system to look at the pull
code in gromacs? I did not find any examples in the WWW,
unfortunately.

Vitaly

--
Dr. Vitaly Chaban





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[gmx-users] pull code example

2010-07-17 Thread Vitaly Chaban

Hi all,

Could anybody please share some working system to look at the pull
code in gromacs? I did not find any examples in the WWW,
unfortunately.

Vitaly

--
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[gmx-users] pull code

2010-07-01 Thread Gavin Melaugh

Hi all

I am using the pull-code to pull two molecules are together which is working. I 
am
however slightly confused about the parameters pull_rate1 and pull_k1. I
want the molecules to come together very slowly therefore
I would set the rate to be a very small value. How the does the force
come into play and how should you decide on the best value?

Cheers
Gavin

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Re: [gmx-users] Pull code

2010-07-01 Thread Gavin Melaugh

Hi Justin

Thanks for your help. The two molecules are now moving together. I am
however slightly confused about the parameters pull_rate1 and pull_k1. I
want the molecules to come together very slowly therefore
I would set the rate to be a very small value. How the does the force
come into play and how should you decide on the best value?

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Hi Justin
>>
>> Thanks. If I use the pull_geometry = direction I would go for the
>> following jus t to pull the molecules together in the z direction.
>>
>> pull= umbrella
>> pull_geometry = direction
>> pull_start = yes
>> pull_ngroups = 1
>> pull_group0 = cage_1
>> pull_group1 = cage_2
>> pull_vec1 = 0.0 0.0 -1.0
>> pull_rate1 = 0.01
>> pull_k1 = 1000
>>
>>
>> Does this seem reasonable? Also in the pull_rate what is meant by the
>
> Probably.  Try it.
>
>> 'rate of change of the reference position'? (Is it the position of the
>> reference group, if so what if I don't want it to change?)
>>
>
> It is the rate of change of the reference position, which is the
> position at the outset of the simulation.  Your objective is to pull
> your two species together, right?  I don't see why you wouldn't want
> it to change.  You're not changing anything about pull_group0 (your
> reference group), since you aren't setting pull_rate0.  Everything is
> applied to pull_group1 (hence _rate1, _k1, etc).
>
> -Justin
>
>> Cheers
>>
>> Gavin
>>
>

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[gmx-users] Pull code

2010-06-30 Thread chris . neale

In addition to what everyone else has said, please note that pull_dim  
= N N Y is going to allow X and Y distance components to get as  
large/small as they will without any restraint. This may be what you  
want, but if you want a distance, but want it to be mostly in Z, then  
pull_dim = Y Y Y and other parameters set appropriately.


Chris.

-- original message --

Gavin Melaugh gmelaugh01 at qub.ac.uk
Wed Jun 30 18:27:47 CEST 2010

* Previous message: [gmx-users] the job is not being distributed
* Next message: [gmx-users] Pull code
* Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

Hi all

I am commencing the initial stages for he calculation of potential of
mean force of bringing together two cage molecules. I am following the
tutorial in such an exercise at
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
In contrast to the tutorial I want to bring the two molecules together
along the z axis. I have generated an initial configuration in which the
COMs of the two molecules are 5.07 nm apart.
In the tutorial to separate a substrate from a protein you use the
following parameters in the mdp file.

; Pull code
pull= umbrella
pull_geometry   = distance
pull_dim= N N Y
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = Chain_B
pull_group1 = Chain_A
pull_rate1  = 0.01  ; 0.01 nm per ps = 10 nm per n
pull_k1 = 1000  ; kJ mol^-1 nm^-


How should I alter this to pull the molecules together along the z axis?
I would've thought the following but I'm not too sure

pull= umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = yes
pull_ngroups = 1
pull_group0 = cage_1
pull_group1 = cage_2
pull_rate1 = -0.01
pull_k1 = 1000


Obviously I have to play with the values, but it is the sign that I'm
interested in.

Many Thanks

Gavin


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Re: [gmx-users] Pull code

2010-06-30 Thread Justin A. Lemkul




Gavin Melaugh wrote:

Hi Justin

Thanks. If I use the pull_geometry = direction I would go for the
following jus t to pull the molecules together in the z direction.

pull= umbrella
pull_geometry = direction
pull_start = yes
pull_ngroups = 1
pull_group0 = cage_1
pull_group1 = cage_2
pull_vec1 = 0.0 0.0 -1.0
pull_rate1 = 0.01
pull_k1 = 1000


Does this seem reasonable? Also in the pull_rate what is meant by the


Probably.  Try it.


'rate of change of the reference position'? (Is it the position of the
reference group, if so what if I don't want it to change?)



It is the rate of change of the reference position, which is the position at the 
outset of the simulation.  Your objective is to pull your two species together, 
right?  I don't see why you wouldn't want it to change.  You're not changing 
anything about pull_group0 (your reference group), since you aren't setting 
pull_rate0.  Everything is applied to pull_group1 (hence _rate1, _k1, etc).


-Justin


Cheers

Gavin



--


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] Pull code

2010-06-30 Thread Gavin Melaugh

Hi Justin

Thanks. If I use the pull_geometry = direction I would go for the
following jus t to pull the molecules together in the z direction.

pull= umbrella
pull_geometry = direction
pull_start = yes
pull_ngroups = 1
pull_group0 = cage_1
pull_group1 = cage_2
pull_vec1 = 0.0 0.0 -1.0
pull_rate1 = 0.01
pull_k1 = 1000


Does this seem reasonable? Also in the pull_rate what is meant by the
'rate of change of the reference position'? (Is it the position of the
reference group, if so what if I don't want it to change?)

Cheers

Gavin
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Re: [gmx-users] Pull code

2010-06-30 Thread Justin A. Lemkul




Gavin Melaugh wrote:

Hi all

I am commencing the initial stages for he calculation of potential of
mean force of bringing together two cage molecules. I am following the
tutorial in such an exercise at
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
In contrast to the tutorial I want to bring the two molecules together
along the z axis. I have generated an initial configuration in which the
COMs of the two molecules are 5.07 nm apart.
In the tutorial to separate a substrate from a protein you use the
following parameters in the mdp file.

; Pull code
pull= umbrella
pull_geometry   = distance
pull_dim= N N Y
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = Chain_B
pull_group1 = Chain_A
pull_rate1  = 0.01  ; 0.01 nm per ps = 10 nm per n
pull_k1 = 1000  ; kJ mol^-1 nm^-


How should I alter this to pull the molecules together along the z axis?
I would've thought the following but I'm not too sure

pull= umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = yes
pull_ngroups = 1
pull_group0 = cage_1
pull_group1 = cage_2
pull_rate1 = -0.01
pull_k1 = 1000


Obviously I have to play with the values, but it is the sign that I'm
interested in.



Have you tried it?  I think it should do what you want.  Otherwise, it is 
probably easier to use "pull_geometry = direction" and specify the actual vector 
along which to pull.  The tutorial is only really useful from a conceptual 
standpoint, and for a system in which pulling is applied in only one direction 
to cause a positive displacement.


-Justin


Many Thanks

Gavin


--


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] Pull code

2010-06-30 Thread Gavin Melaugh

Hi all

I am commencing the initial stages for he calculation of potential of
mean force of bringing together two cage molecules. I am following the
tutorial in such an exercise at
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
In contrast to the tutorial I want to bring the two molecules together
along the z axis. I have generated an initial configuration in which the
COMs of the two molecules are 5.07 nm apart.
In the tutorial to separate a substrate from a protein you use the
following parameters in the mdp file.

; Pull code
pull= umbrella
pull_geometry   = distance
pull_dim= N N Y
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = Chain_B
pull_group1 = Chain_A
pull_rate1  = 0.01  ; 0.01 nm per ps = 10 nm per n
pull_k1 = 1000  ; kJ mol^-1 nm^-


How should I alter this to pull the molecules together along the z axis?
I would've thought the following but I'm not too sure

pull= umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = yes
pull_ngroups = 1
pull_group0 = cage_1
pull_group1 = cage_2
pull_rate1 = -0.01
pull_k1 = 1000


Obviously I have to play with the values, but it is the sign that I'm
interested in.

Many Thanks

Gavin
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RE: [gmx-users] pull code with defined negative relative displacements

2009-11-18 Thread Berk Hess


Hi,

With only 1 pull dimension active (through pull_dims) all three geometries are 
equivalent.
In 2 or 3D there are all different.

With pull_geometry=direction the pull force is the force working along the 
direction vector.
So in general you can't incorporate the direction (only sign in your case) into 
the force,
unless you would print the whole vector.

Berk

> Date: Wed, 18 Nov 2009 12:12:49 -0500
> From: chris.ne...@utoronto.ca
> To: gmx-users@gromacs.org
> Subject: [gmx-users] pull code with defined negative relative displacements
> 
> Hi Berk,
> 
> I have done the tests and you are entirely correct. I have one further  
> question: If I simply want to pull to a relative displacement of -1.0  
> nm, is there any reason to prefer one of these methods, or are they  
> just overlapping implementations of different methods that also have  
> unique abilities given other settings?
> 
> To summarize my tests, pull_geometry=direction can indeed pull to negative  
> displacements and there is no bimodal behaviour. My misunderstanding  
> derived from the fact that
> 
> pull_geometry= direction
> pull_init1   = 1.0
> pull_vec1= 0 0 1
> 
> gave the forces as I expected them, while
> 
> pull_vec1= 0 0 -1
> 
> reports the negative of the force that I expected. Since the force as  
> output is probably applied after multiplication by pull_vec1, it might  
> be more intuitive to simply output the force after it is multiplied by  
> pull_vec1 such that what is output is the actual applied force. But  
> then again there are probably some good reasons why it is output the  
> way that it is.
> 
> I have included probability distribution plots for the sampling along z for 
> the tests below at:
> http://i205.photobucket.com/albums/bb192/chrisneale_2007/X10.png  (1.0 nm 
> displacement test)
> http://i205.photobucket.com/albums/bb192/chrisneale_2007/X005.png  (0.05 nm 
> displacement test)
> http://i205.photobucket.com/albums/bb192/chrisneale_2007/X35.png  (3.5 nm 
> displacement test)
> 
> Thank you for all of your assistance,
> Chris.
>  
> #
> Summary for attempts to pull to -1.0:
> 
> ### Pulls to -1
> 
> pull_geometry= position
> pull_init1   = 0 0 -1
> pull_vec1= 0 0 0
> 
> pull_geometry= direction
> pull_init1   = -1.0
> pull_vec1= 0 0 1
> 
> pull_geometry= direction
> pull_init1   = 1.0
> pull_vec1= 0 0 -1
> 
> ### Pulls to +1
> 
> pull_geometry= direction
> pull_init1   = 1.0
> pull_vec1= 0 0 1
> 
> #
> Detailed results:
> 
> pull_geometry= position
> pull_init1   = 0 0 -1
> pull_vec1= 0 0 0
> 
> $ tail coord.xvg
> 98.2000   5.03064 -0.96114
> 98.4000   5.02906 -0.968864
> 98.6000   5.02755 -1.0196
> 98.8000   5.02577 -0.971355
> 99.   5.02408 -0.948518
> 99.2000   5.02289 -0.973627
> 99.4000   5.0227  -0.977471
> 99.6000   5.02293 -0.965711
> 99.8000   5.0242  -1.01475
> 100.  5.0251  -1.03216
> 
> $ tail force.xvg
> 98.2000   -19.4299
> 98.4000   -15.568
> 98.6000   9.8014
> 98.8000   -14.3227
> 99.   -25.741
> 99.2000   -13.1865
> 99.4000   -11.2644
> 99.6000   -17.1443
> 99.8000   7.37747
> 100.  16.0813
> 
> 
> 
> pull_geometry= direction
> pull_init1   = 1.0
> pull_vec1= 0 0 1
> 
> $ tail coord.xvg
> 98.2000   5.06691 1.09005
> 98.4000   5.06773 1.04829
> 98.6000   5.06842 1.02481
> 98.8000   5.06934 1.02874
> 99.   5.07061 0.995157
> 99.2000   5.07164 0.990872
> 99.4000   5.07205 1.00651
> 99.6000   5.07256 1.02346
> 99.8000   5.07107 0.986439
> 100.  5.06931 1.03009
> 
> $ tail force.xvg
> 98.2000   -45.0273
> 98.4000   -24.1432
> 98.6000   -12.4043
> 98.8000   -14.3716
> 99.   2.42147
> 99.2000   4.56404
> 99.4000   -3.25742
> 99.6000   -11.7324
> 99.8000   6.78027
> 100.  -15.0443
> 
> ### where it does start at -1.0
> 
> $ grep -v '[#|@]' coord.xvg |head
> 0.5.05992 -1.09968
> 0.20005.05948 -0.473992
> 0.40005.05982 0.43101
> 0.60005.06017 0.77986
> 0.80005.0609  0.78875
> 1.5.06113 0.75552
> 1.20005.06151 0.750633
> 1.40005.06086 0.7

[gmx-users] pull code with defined negative relative displacements

2009-11-18 Thread Chris Neale


Hi Berk,

I have done the tests and you are entirely correct. I have one further  
question: If I simply want to pull to a relative displacement of -1.0  
nm, is there any reason to prefer one of these methods, or are they  
just overlapping implementations of different methods that also have  
unique abilities given other settings?


To summarize my tests, pull_geometry=direction can indeed pull to negative  
displacements and there is no bimodal behaviour. My misunderstanding  
derived from the fact that


pull_geometry= direction
pull_init1   = 1.0
pull_vec1= 0 0 1

gave the forces as I expected them, while

pull_vec1= 0 0 -1

reports the negative of the force that I expected. Since the force as  
output is probably applied after multiplication by pull_vec1, it might  
be more intuitive to simply output the force after it is multiplied by  
pull_vec1 such that what is output is the actual applied force. But  
then again there are probably some good reasons why it is output the  
way that it is.


I have included probability distribution plots for the sampling along z for the 
tests below at:
http://i205.photobucket.com/albums/bb192/chrisneale_2007/X10.png  (1.0 nm 
displacement test)
http://i205.photobucket.com/albums/bb192/chrisneale_2007/X005.png  (0.05 nm 
displacement test)
http://i205.photobucket.com/albums/bb192/chrisneale_2007/X35.png  (3.5 nm 
displacement test)

Thank you for all of your assistance,
Chris.

#
Summary for attempts to pull to -1.0:

### Pulls to -1

pull_geometry= position
pull_init1   = 0 0 -1
pull_vec1= 0 0 0

pull_geometry= direction
pull_init1   = -1.0
pull_vec1= 0 0 1

pull_geometry= direction
pull_init1   = 1.0
pull_vec1= 0 0 -1

### Pulls to +1

pull_geometry= direction
pull_init1   = 1.0
pull_vec1= 0 0 1

#
Detailed results:

pull_geometry= position
pull_init1   = 0 0 -1
pull_vec1= 0 0 0

$ tail coord.xvg
98.2000 5.03064 -0.96114
98.4000 5.02906 -0.968864
98.6000 5.02755 -1.0196
98.8000 5.02577 -0.971355
99. 5.02408 -0.948518
99.2000 5.02289 -0.973627
99.4000 5.0227  -0.977471
99.6000 5.02293 -0.965711
99.8000 5.0242  -1.01475
100.5.0251  -1.03216

$ tail force.xvg
98.2000 -19.4299
98.4000 -15.568
98.6000 9.8014
98.8000 -14.3227
99. -25.741
99.2000 -13.1865
99.4000 -11.2644
99.6000 -17.1443
99.8000 7.37747
100.16.0813



pull_geometry= direction
pull_init1   = 1.0
pull_vec1= 0 0 1

$ tail coord.xvg
98.2000 5.06691 1.09005
98.4000 5.06773 1.04829
98.6000 5.06842 1.02481
98.8000 5.06934 1.02874
99. 5.07061 0.995157
99.2000 5.07164 0.990872
99.4000 5.07205 1.00651
99.6000 5.07256 1.02346
99.8000 5.07107 0.986439
100.5.06931 1.03009

$ tail force.xvg
98.2000 -45.0273
98.4000 -24.1432
98.6000 -12.4043
98.8000 -14.3716
99. 2.42147
99.2000 4.56404
99.4000 -3.25742
99.6000 -11.7324
99.8000 6.78027
100.-15.0443

### where it does start at -1.0

$ grep -v '[#|@]' coord.xvg |head
0.  5.05992 -1.09968
0.2000  5.05948 -0.473992
0.4000  5.05982 0.43101
0.6000  5.06017 0.77986
0.8000  5.0609  0.78875
1.  5.06113 0.75552
1.2000  5.06151 0.750633
1.4000  5.06086 0.79958
1.6000  5.05976 0.821069
1.8000  5.05811 0.950296

###

pull_geometry= direction
pull_init1   = -1.0
pull_vec1= 0 0 1

$ tail -n 30 coord.xvg|head -n 10
94.2000 5.04636 -1.00959
94.4000 5.04605 -1.09414
94.6000 5.04503 -1.09134
94.8000 5.0431  -1.10409
95. 5.04174 -1.05292
95.2000 5.04012 -1.03421
95.4000 5.03944 -1.05723
95.6000 5.03981 -1.00803
95.8000 5.04072 -1.01506
96. 5.04055 -0.980655

$ tail -n 30 force.xvg|head -n 10
94.2000 4.79288
94.4000 47.0722
94.6000 45.6695
94.8000 52.0426
95. 26.4623
95.2000 17.107
95.4000 28.6127
95.6000 4.0165
95.8000 7.52866
96. -9.67265

###

pull_geometry= direction
pull_init1   = 1.0
pull_vec1= 0 0 -1

$ tail coord.xvg
98.2000 5.01781 -1.04195
98.4000 5.01766 -0.988034
98.6000 5.01789 -0.963644
98.8000 5.0185  -0.980899
99. 5.01958 -0.917222
99.2000 5.021   -1.00548
99.4000 5.02016 -0.970434
99.6000 5.01848 -1.01137
99.8000 5.01723 -0.950541
100.5.01743 -1.01916

$ tail force.xvg
98.2000 -20.9744
98.4000 5.98316
98.6000 18.1779
98.8000 9.55039
99. 41.3892
99.2000 -2.73847
99.4000 14.7832
99.6000 -5.68352
99.8000 24.7297
100.-9.58189

#
#
#
#

Summary for attempts to pull to -0.1:

### Pulls to -0.1

pull_geometry= position
pull_init1   = 0 0 -0.1
pull_vec1

RE: [gmx-users] pull code with defined negative relative displacements


Hi,

I would still say pull_geometry=direction would be the easiest solution for 
this case,
but pull_geometry=position will probably do the same thing.

Berk

> Date: Sun, 15 Nov 2009 17:11:43 -0500
> From: chris.ne...@utoronto.ca
> To: gmx-users@gromacs.org
> Subject: [gmx-users] pull code with defined negative relative displacements
> 
> Hi Berk,
> 
> I do not mean the box 0, and I am aware about the pull distance  
> needing to be less than half of the smallest box length. Please allow  
> me describe a bit more rigorously what I need to avoid. I will use an  
> example that is totally fictitious, but is designed to emphasize the  
> bimodal sampling issue that is relevant to my actual study.
> 
> 1. Imagine that one wants to calculate the PMF for a water molecule  
> along the normal to an asymmetric bilayer in which one leaflet is POPC  
> and the other is lipidA.
> 
> 2. The free energy for that water residing 0.1 nm away from the  
> bilayer center in the POPC leaflet (call it -0.1 nm from the bilayer  
> center) needs to be calculated separately from the free energy for  
> that water residing 0.1 nm away from the bilayer center in the lipidA  
> leaflet (call it +0.1 nm from the bilayer center).
> 
> 3. Let the force constant be 500 kJ/mol/nm^2 and let the user apply  
> pull_geometry=distance and pull_init1=0.1 while starting the replica  
> at 0.1 nm from the bilayer center in two simulations where one takes  
> (a) a starting water position that is 0.1 nm toward the POPC  
> headgroups and the other takes (b) a starting position of the water to  
> be 0.1 nm toward the lipidA headgroups.
> 
> 4. I posit that the probability distributions of the water about the  
> bilayer normal from simulations (a) and (b) in part 3 above will  
> converge to the same distribution and that this distribution will be  
> bimodal with one peak at -0.1 nm and one peak at +0.1 nm. This is  
> because the simulation that started at -0.1 (0.1 nm closer to the POPC  
> headgroups) will, even under the biasing force, infrequently cross the  
> bilayer center of mass and then be closer to the lipidA heagroups. At  
> this point. the direction of the applied force will the change to draw  
> the water toward the other possible location at +0.1 nm.
> 
> 5a. For displacements >> 0.1 nm, this will not be a problem.
> 5b. For larger force constants, this will not be a problem at 0.1 nm,  
> but will still be a problem for some closer centers of restraint.
> 
> 6. pull_geometry=distance is entirely incompatible with this approach.
> 
> 7. pull_geometry=position does appear to work.
> 
> 
> Thanks for your patience,
> Chris.
> 
> -- original message --
> 
> Hi,
> 
> Sorry, but I have no clue what you mean with sampling >0
> and how you would end up with a bimodal distribution.
> 
> You don't mean the box 0, do you?
> That is irrelevant.
> What can be a problem is that you pull distance should not be more  
> than half the box length.
> 
> Berk
> 
> > Date: Sun, 15 Nov 2009 12:33:30 -0500
> > From: chris.neale at utoronto.ca
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] pull code with defined negative relative displacements
> >
> > > I only now noticed Justin mail on g_wham.
> > > You can probably also use pull_geometry=distance and pull_init=1,
> > > if you starting structure has group1 close to 1 nm below group 0.
> >
> > Agreed, although this will not work when the force constant is not   
> > strong enough to inhibit any sampling >0 -- wherein the distribution  
> >  about 0 would become bimodal and this is something that I can not  
> > allow.
> >
> > As far as I can tell, pull_geometry=position, pull_init1<0, and   
> > pull_vec1=0 0 0 is the solution, as per my previous message.
> >
> > Thank you,
> > Chris.
> 
> 
> -- 
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[gmx-users] pull code with defined negative relative displacements

2009-11-15 Thread chris . neale


Hi Berk,

I do not mean the box 0, and I am aware about the pull distance  
needing to be less than half of the smallest box length. Please allow  
me describe a bit more rigorously what I need to avoid. I will use an  
example that is totally fictitious, but is designed to emphasize the  
bimodal sampling issue that is relevant to my actual study.


1. Imagine that one wants to calculate the PMF for a water molecule  
along the normal to an asymmetric bilayer in which one leaflet is POPC  
and the other is lipidA.


2. The free energy for that water residing 0.1 nm away from the  
bilayer center in the POPC leaflet (call it -0.1 nm from the bilayer  
center) needs to be calculated separately from the free energy for  
that water residing 0.1 nm away from the bilayer center in the lipidA  
leaflet (call it +0.1 nm from the bilayer center).


3. Let the force constant be 500 kJ/mol/nm^2 and let the user apply  
pull_geometry=distance and pull_init1=0.1 while starting the replica  
at 0.1 nm from the bilayer center in two simulations where one takes  
(a) a starting water position that is 0.1 nm toward the POPC  
headgroups and the other takes (b) a starting position of the water to  
be 0.1 nm toward the lipidA headgroups.


4. I posit that the probability distributions of the water about the  
bilayer normal from simulations (a) and (b) in part 3 above will  
converge to the same distribution and that this distribution will be  
bimodal with one peak at -0.1 nm and one peak at +0.1 nm. This is  
because the simulation that started at -0.1 (0.1 nm closer to the POPC  
headgroups) will, even under the biasing force, infrequently cross the  
bilayer center of mass and then be closer to the lipidA heagroups. At  
this point. the direction of the applied force will the change to draw  
the water toward the other possible location at +0.1 nm.


5a. For displacements >> 0.1 nm, this will not be a problem.
5b. For larger force constants, this will not be a problem at 0.1 nm,  
but will still be a problem for some closer centers of restraint.


6. pull_geometry=distance is entirely incompatible with this approach.

7. pull_geometry=position does appear to work.


Thanks for your patience,
Chris.

-- original message --

Hi,

Sorry, but I have no clue what you mean with sampling >0
and how you would end up with a bimodal distribution.

You don't mean the box 0, do you?
That is irrelevant.
What can be a problem is that you pull distance should not be more  
than half the box length.


Berk


Date: Sun, 15 Nov 2009 12:33:30 -0500
From: chris.neale at utoronto.ca
To: gmx-users at gromacs.org
Subject: [gmx-users] pull code with defined negative relative displacements

> I only now noticed Justin mail on g_wham.
> You can probably also use pull_geometry=distance and pull_init=1,
> if you starting structure has group1 close to 1 nm below group 0.

Agreed, although this will not work when the force constant is not   
strong enough to inhibit any sampling >0 -- wherein the distribution  
 about 0 would become bimodal and this is something that I can not  
allow.


As far as I can tell, pull_geometry=position, pull_init1<0, and   
pull_vec1=0 0 0 is the solution, as per my previous message.


Thank you,
Chris.



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RE: [gmx-users] pull code with defined negative relative displacements


Hi,

Sorry, but I have no clue what you mean with sampling >0
and how you would end up with a bimodal distribution.

You don't mean the box 0, do you?
That is irrelevant.
What can be a problem is that you pull distance should not be more than half 
the box length.

Berk

> Date: Sun, 15 Nov 2009 12:33:30 -0500
> From: chris.ne...@utoronto.ca
> To: gmx-users@gromacs.org
> Subject: [gmx-users] pull code with defined negative relative displacements
> 
> > I only now noticed Justin mail on g_wham.
> > You can probably also use pull_geometry=distance and pull_init=1,
> > if you starting structure has group1 close to 1 nm below group 0.
> 
> Agreed, although this will not work when the force constant is not  
> strong enough to inhibit any sampling >0 -- wherein the distribution  
> about 0 would become bimodal and this is something that I can not allow.
> 
> As far as I can tell, pull_geometry=position, pull_init1<0, and  
> pull_vec1=0 0 0 is the solution, as per my previous message.
> 
> Thank you,
> Chris.
> 
> 
> 
> -- 
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[gmx-users] pull code with defined negative relative displacements

2009-11-15 Thread chris . neale


I only now noticed Justin mail on g_wham.
You can probably also use pull_geometry=distance and pull_init=1,
if you starting structure has group1 close to 1 nm below group 0.


Agreed, although this will not work when the force constant is not  
strong enough to inhibit any sampling >0 -- wherein the distribution  
about 0 would become bimodal and this is something that I can not allow.


As far as I can tell, pull_geometry=position, pull_init1<0, and  
pull_vec1=0 0 0 is the solution, as per my previous message.


Thank you,
Chris.



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[gmx-users] pull code with defined negative relative displacements

2009-11-15 Thread chris . neale

Hi Berk, I am aware that pull_init=4.75 should pull to 4.75, not 1.0.  
I was mixing results from my simulations as I was discussing, sorry.


Please allow me to restate the issue: If I am indeed pulling to 4.75  
below group 0, then why is the force positive when group 1 has a  
displacement of -4.68988 (see below):


coord.xvg:
1669.4000   4.97979 -4.68988
force.xvg:
1669.4000   30.0622

I think that pull_geometry=distance and pull_geometry=direction are  
not going to work here.


I have moved to a test system that is the a box of water in which I  
pull the z of one water to a relative displacement with respect to one  
other water.


From this, I have found that pull_geometry=position while passing in  
a negative pull_init1 and a pull_vec1 of 0 0 0, appears to be the only  
way to get this done.


Thank you for all of your time,
Chris.


Hi,

pull_init should be 1, not 4.75, if you want group1 to be 1 nm below group0.
Alternatively you can have vec = 0 0 1 and pull_init = -1.

Berk


Date: Sat, 14 Nov 2009 14:54:54 -0500
From: chris.ne...@utoronto.ca
To: gmx-users@gromacs.org
Subject: [gmx-users] pull code with defined negative relative displacements

Hi Justin, (comment to Berk below)

thanks for pointing out the g_wham problem. I am personally ok here as
I use a non-gromacs wham program.

Hi Berk,

unless I misunderstood, your suggestion does not yield the gromacs 3
behaviour that I am trying to reproduce with gromacs 4.

If I simply misunderstood your suggestion, can you please be a little
more explicit? What I want to do is to harmonically restrain the COM
of group 1 to be X nm more negative along Z than the COM of group 0.
It is important that this still works when the value for X is smaller
than the standard deviation of the sampled values such that the
distribution does not become bimodal.

Here is the test using pull_geometry=direction, and I note that this
is exactly the same behaviour that I observed and posted in my last
email while using pull_geometry=distance in combination with pull_vec.

pull = umbrella
pull_geometry= direction
pull_dim = N N Y
pull_start   = no
pull_nstxout = 10
pull_nstfout = 10
pull_ngroups = 1
pull_group0  = POPC
pull_pbcatom0= 0
pull_group1  = Protein
pull_pbcatom1= 0
pull_init1   = 4.75
pull_rate1   = 0
pull_k1  = 500.0
pull_vec1   = 0 0 -1


coord.xvg:
1669.4000   4.97979 -4.68988
force.xvg:
1669.4000   30.0622
Where the force should be -30.062 (assuming that I understand
everything correctly).

coord.xvg:
2.9600  5.16151 -5.14321
force.xvg
2.9600  -196.603
Where the force should be +196.603 (assuming that I understand
everything correctly).

pull = umbrella
pull_geometry= direction
pull_dim = N N Y
pull_start   = no
pull_nstxout = 10
pull_nstfout = 10
pull_ngroups = 1
pull_group0  = POPC
pull_pbcatom0= 0
pull_group1  = Protein
pull_pbcatom1= 0
pull_init1   = 4.75
pull_rate1   = 0
pull_k1  = 500.0
pull_vec1   = 0 0 1

coord.xvg:
0.5200  5.17421 5.00621
force.xvg:
0.5200  -128.107
Where this is what I intend to occur (i.e. working as I desire it to).

coord.xvg:
1649.4000   4.99895 4.69239
force.xvg:
1649.4000   28.807
Where this is what I intend to occur (i.e. working as I desire it to).




Thank you,
Chris.

--- original message --

Hi,

You should use pull_geometry=direction.
distances don't get negative.

Berk

> Date: Sat, 14 Nov 2009 09:21:39 -0500
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] pull code with defined negative relative   
displacements

>
> Hello, I am re-running some of our gromacs 3 simulations using gromacs
> 4, and as far as I can tell the gromacs 4 pull code, while very nicely
> enhanced from gromacs 3, has also lost some functionality.
>
> I am calculating the PMF of a peptide across a bilayer and, to
> simplify the issue, what I can't figure out how to do with gromacs 4
>  is to pull group1 to a position 1 nm more negative along the z-axis
>  than group 0 (the bilayer in this case) for some replicas and to 1
> nm  more positive along the z-axis than group 0 in others. I'll
> focus on  the negative displacement here as it is the one that is
> giving me  problems.
>
> This used to be possible with the following gromacs 3 pull.ppa options:
>
> runtype   = umbrella
> reftype   = com
> pulldim   = N N Y
> reference_group = group0
> group_1   = group1
> K1= 500
> Pos1  = 0 0 -1.0
>
> Sure, I could start group1 in the correct negative-z displacement from
> group0 and use

RE: [gmx-users] pull code with defined negative relative displacements


Hi,

I only now noticed Justin mail on g_wham.
You can probably also use pull_geometry=distance and pull_init=1,
if you starting structure has group1 close to 1 nm below group 0.

Berk

From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] pull code with defined negative relative displacements
Date: Sun, 15 Nov 2009 12:10:28 +0100








Hi,

pull_init should be 1, not 4.75, if you want group1 to be 1 nm below group0.
Alternatively you can have vec = 0 0 1 and pull_init = -1.

Berk

> Date: Sat, 14 Nov 2009 14:54:54 -0500
> From: chris.ne...@utoronto.ca
> To: gmx-users@gromacs.org
> Subject: [gmx-users] pull code with defined negative relative displacements
> 
> Hi Justin, (comment to Berk below)
> 
> thanks for pointing out the g_wham problem. I am personally ok here as  
> I use a non-gromacs wham program.
> 
> Hi Berk,
> 
> unless I misunderstood, your suggestion does not yield the gromacs 3  
> behaviour that I am trying to reproduce with gromacs 4.
> 
> If I simply misunderstood your suggestion, can you please be a little  
> more explicit? What I want to do is to harmonically restrain the COM  
> of group 1 to be X nm more negative along Z than the COM of group 0.  
> It is important that this still works when the value for X is smaller  
> than the standard deviation of the sampled values such that the  
> distribution does not become bimodal.
> 
> Here is the test using pull_geometry=direction, and I note that this  
> is exactly the same behaviour that I observed and posted in my last  
> email while using pull_geometry=distance in combination with pull_vec.
> 
> pull = umbrella
> pull_geometry= direction
> pull_dim = N N Y
> pull_start   = no
> pull_nstxout = 10
> pull_nstfout = 10
> pull_ngroups = 1
> pull_group0  = POPC
> pull_pbcatom0= 0
> pull_group1  = Protein
> pull_pbcatom1= 0
> pull_init1   = 4.75
> pull_rate1   = 0
> pull_k1  = 500.0
> pull_vec1   = 0 0 -1
> 
> 
> coord.xvg:
> 1669.4000   4.97979 -4.68988
> force.xvg:
> 1669.4000   30.0622
> Where the force should be -30.062 (assuming that I understand  
> everything correctly).
> 
> coord.xvg:
> 2.9600  5.16151 -5.14321
> force.xvg
> 2.9600  -196.603
> Where the force should be +196.603 (assuming that I understand  
> everything correctly).
> 
> pull = umbrella
> pull_geometry= direction
> pull_dim = N N Y
> pull_start   = no
> pull_nstxout = 10
> pull_nstfout = 10
> pull_ngroups = 1
> pull_group0  = POPC
> pull_pbcatom0= 0
> pull_group1  = Protein
> pull_pbcatom1= 0
> pull_init1   = 4.75
> pull_rate1   = 0
> pull_k1  = 500.0
> pull_vec1   = 0 0 1
> 
> coord.xvg:
> 0.5200  5.17421 5.00621
> force.xvg:
> 0.5200  -128.107
> Where this is what I intend to occur (i.e. working as I desire it to).
> 
> coord.xvg:
> 1649.4000   4.99895 4.69239
> force.xvg:
> 1649.4000   28.807
> Where this is what I intend to occur (i.e. working as I desire it to).
> 
> 
> 
> 
> Thank you,
> Chris.
> 
> --- original message --
> 
> Hi,
> 
> You should use pull_geometry=direction.
> distances don't get negative.
> 
> Berk
> 
> > Date: Sat, 14 Nov 2009 09:21:39 -0500
> > From: chris.neale at utoronto.ca
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] pull code with defined negative relative displacements
> >
> > Hello, I am re-running some of our gromacs 3 simulations using gromacs
> > 4, and as far as I can tell the gromacs 4 pull code, while very nicely
> > enhanced from gromacs 3, has also lost some functionality.
> >
> > I am calculating the PMF of a peptide across a bilayer and, to   
> > simplify the issue, what I can't figure out how to do with gromacs 4  
> >  is to pull group1 to a position 1 nm more negative along the z-axis  
> >  than group 0 (the bilayer in this case) for some replicas and to 1  
> > nm  more positive along the z-axis than group 0 in others. I'll  
> > focus on  the negative displacement here as it is the one that is  
> > giving me  problems.
> >
> > This used to be possible with the following gromacs 3 pull.ppa options:
> >
> > runtype   = umbrella
> > reftype   = com
> > pulldim   = N N Y
> > reference_group = group0
> > group

RE: [gmx-users] pull code with defined negative relative displacements


Hi,

pull_init should be 1, not 4.75, if you want group1 to be 1 nm below group0.
Alternatively you can have vec = 0 0 1 and pull_init = -1.

Berk

> Date: Sat, 14 Nov 2009 14:54:54 -0500
> From: chris.ne...@utoronto.ca
> To: gmx-users@gromacs.org
> Subject: [gmx-users] pull code with defined negative relative displacements
> 
> Hi Justin, (comment to Berk below)
> 
> thanks for pointing out the g_wham problem. I am personally ok here as  
> I use a non-gromacs wham program.
> 
> Hi Berk,
> 
> unless I misunderstood, your suggestion does not yield the gromacs 3  
> behaviour that I am trying to reproduce with gromacs 4.
> 
> If I simply misunderstood your suggestion, can you please be a little  
> more explicit? What I want to do is to harmonically restrain the COM  
> of group 1 to be X nm more negative along Z than the COM of group 0.  
> It is important that this still works when the value for X is smaller  
> than the standard deviation of the sampled values such that the  
> distribution does not become bimodal.
> 
> Here is the test using pull_geometry=direction, and I note that this  
> is exactly the same behaviour that I observed and posted in my last  
> email while using pull_geometry=distance in combination with pull_vec.
> 
> pull = umbrella
> pull_geometry= direction
> pull_dim = N N Y
> pull_start   = no
> pull_nstxout = 10
> pull_nstfout = 10
> pull_ngroups = 1
> pull_group0  = POPC
> pull_pbcatom0= 0
> pull_group1  = Protein
> pull_pbcatom1= 0
> pull_init1   = 4.75
> pull_rate1   = 0
> pull_k1  = 500.0
> pull_vec1   = 0 0 -1
> 
> 
> coord.xvg:
> 1669.4000   4.97979 -4.68988
> force.xvg:
> 1669.4000   30.0622
> Where the force should be -30.062 (assuming that I understand  
> everything correctly).
> 
> coord.xvg:
> 2.9600  5.16151 -5.14321
> force.xvg
> 2.9600  -196.603
> Where the force should be +196.603 (assuming that I understand  
> everything correctly).
> 
> pull = umbrella
> pull_geometry= direction
> pull_dim = N N Y
> pull_start   = no
> pull_nstxout = 10
> pull_nstfout = 10
> pull_ngroups = 1
> pull_group0  = POPC
> pull_pbcatom0= 0
> pull_group1  = Protein
> pull_pbcatom1= 0
> pull_init1   = 4.75
> pull_rate1   = 0
> pull_k1  = 500.0
> pull_vec1   = 0 0 1
> 
> coord.xvg:
> 0.5200  5.17421 5.00621
> force.xvg:
> 0.5200  -128.107
> Where this is what I intend to occur (i.e. working as I desire it to).
> 
> coord.xvg:
> 1649.4000   4.99895 4.69239
> force.xvg:
> 1649.4000   28.807
> Where this is what I intend to occur (i.e. working as I desire it to).
> 
> 
> 
> 
> Thank you,
> Chris.
> 
> --- original message --
> 
> Hi,
> 
> You should use pull_geometry=direction.
> distances don't get negative.
> 
> Berk
> 
> > Date: Sat, 14 Nov 2009 09:21:39 -0500
> > From: chris.neale at utoronto.ca
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] pull code with defined negative relative displacements
> >
> > Hello, I am re-running some of our gromacs 3 simulations using gromacs
> > 4, and as far as I can tell the gromacs 4 pull code, while very nicely
> > enhanced from gromacs 3, has also lost some functionality.
> >
> > I am calculating the PMF of a peptide across a bilayer and, to   
> > simplify the issue, what I can't figure out how to do with gromacs 4  
> >  is to pull group1 to a position 1 nm more negative along the z-axis  
> >  than group 0 (the bilayer in this case) for some replicas and to 1  
> > nm  more positive along the z-axis than group 0 in others. I'll  
> > focus on  the negative displacement here as it is the one that is  
> > giving me  problems.
> >
> > This used to be possible with the following gromacs 3 pull.ppa options:
> >
> > runtype   = umbrella
> > reftype   = com
> > pulldim   = N N Y
> > reference_group = group0
> > group_1   = group1
> > K1= 500
> > Pos1  = 0 0 -1.0
> >
> > Sure, I could start group1 in the correct negative-z displacement from
> > group0 and use pull_init1=+1.0, but this will not work when, for
> > instance, I want to restrain it to -0.1 nm (using pull_init1=+0.1),
> > where the sampling will infrequently jump back and f

[gmx-users] pull code with defined negative relative displacements

2009-11-14 Thread chris . neale


Hi Justin, (comment to Berk below)

thanks for pointing out the g_wham problem. I am personally ok here as  
I use a non-gromacs wham program.


Hi Berk,

unless I misunderstood, your suggestion does not yield the gromacs 3  
behaviour that I am trying to reproduce with gromacs 4.


If I simply misunderstood your suggestion, can you please be a little  
more explicit? What I want to do is to harmonically restrain the COM  
of group 1 to be X nm more negative along Z than the COM of group 0.  
It is important that this still works when the value for X is smaller  
than the standard deviation of the sampled values such that the  
distribution does not become bimodal.


Here is the test using pull_geometry=direction, and I note that this  
is exactly the same behaviour that I observed and posted in my last  
email while using pull_geometry=distance in combination with pull_vec.


pull = umbrella
pull_geometry= direction
pull_dim = N N Y
pull_start   = no
pull_nstxout = 10
pull_nstfout = 10
pull_ngroups = 1
pull_group0  = POPC
pull_pbcatom0= 0
pull_group1  = Protein
pull_pbcatom1= 0
pull_init1   = 4.75
pull_rate1   = 0
pull_k1  = 500.0
pull_vec1   = 0 0 -1


coord.xvg:
1669.4000   4.97979 -4.68988
force.xvg:
1669.4000   30.0622
Where the force should be -30.062 (assuming that I understand  
everything correctly).


coord.xvg:
2.9600  5.16151 -5.14321
force.xvg
2.9600  -196.603
Where the force should be +196.603 (assuming that I understand  
everything correctly).


pull = umbrella
pull_geometry= direction
pull_dim = N N Y
pull_start   = no
pull_nstxout = 10
pull_nstfout = 10
pull_ngroups = 1
pull_group0  = POPC
pull_pbcatom0= 0
pull_group1  = Protein
pull_pbcatom1= 0
pull_init1   = 4.75
pull_rate1   = 0
pull_k1  = 500.0
pull_vec1   = 0 0 1

coord.xvg:
0.5200  5.17421 5.00621
force.xvg:
0.5200  -128.107
Where this is what I intend to occur (i.e. working as I desire it to).

coord.xvg:
1649.4000   4.99895 4.69239
force.xvg:
1649.4000   28.807
Where this is what I intend to occur (i.e. working as I desire it to).




Thank you,
Chris.

--- original message --

Hi,

You should use pull_geometry=direction.
distances don't get negative.

Berk


Date: Sat, 14 Nov 2009 09:21:39 -0500
From: chris.neale at utoronto.ca
To: gmx-users at gromacs.org
Subject: [gmx-users] pull code with defined negative relative displacements

Hello, I am re-running some of our gromacs 3 simulations using gromacs
4, and as far as I can tell the gromacs 4 pull code, while very nicely
enhanced from gromacs 3, has also lost some functionality.

I am calculating the PMF of a peptide across a bilayer and, to   
simplify the issue, what I can't figure out how to do with gromacs 4  
 is to pull group1 to a position 1 nm more negative along the z-axis  
 than group 0 (the bilayer in this case) for some replicas and to 1  
nm  more positive along the z-axis than group 0 in others. I'll  
focus on  the negative displacement here as it is the one that is  
giving me  problems.


This used to be possible with the following gromacs 3 pull.ppa options:

runtype   = umbrella
reftype   = com
pulldim   = N N Y
reference_group = group0
group_1   = group1
K1= 500
Pos1  = 0 0 -1.0

Sure, I could start group1 in the correct negative-z displacement from
group0 and use pull_init1=+1.0, but this will not work when, for
instance, I want to restrain it to -0.1 nm (using pull_init1=+0.1),
where the sampling will infrequently jump back and forth about z=0.

Just to be sure, I tried for gromacs 4 are the following pull code   
.mdp options:


pull = umbrella
pull_geometry= distance
pull_dim = N N Y
pull_start   = no
pull_ngroups = 1
pull_group0  = group0
pull_group1  = group1
pull_init1   = -1.0
pull_rate1   = 0
pull_k1  = 500.0

where mdrun complains:
"Pull reference distance for group 1 is negative (-1.00)"

and it is pretty obvious why this doesn't work since it is asking for
a negative displacement. Nevertheless, I tried it and pull_init1
appears to get set to zero.

I also attempted the following.

pull = umbrella
pull_geometry= distance
pull_dim = N N Y
pull_start   = no
pull_ngroups = 1
pull_group0  = group0
pull_group1  = group1
pull_init1   = 1.0
pull_rate1   = 0
pull_k1  = 500.0
pull_vec1= 0 0 -1

where I would then use
pull_init

Re: [gmx-users] pull code with defined negative relative displacements

2009-11-14 Thread Justin A. Lemkul




Berk Hess wrote:

Hi,

You should use pull_geometry=direction.
distances don't get negative.


I think this presents a problem if one is intending to use g_wham to calculate 
PMF from the umbrella sampling protocol.  When using direction for 
pull_geometry, g_wham fails with a fatal error:


---
Program g_wham, VERSION 4.0.5
Source code file: gmx_wham.c, line: 1337

Fatal error:
Pull geometry direction not supported

---

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] pull code with defined negative relative displacements

2009-11-14 Thread Berk Hess


Hi,

You should use pull_geometry=direction.
distances don't get negative.

Berk

> Date: Sat, 14 Nov 2009 09:21:39 -0500
> From: chris.ne...@utoronto.ca
> To: gmx-users@gromacs.org
> Subject: [gmx-users] pull code with defined negative relative displacements
> 
> Hello, I am re-running some of our gromacs 3 simulations using gromacs
> 4, and as far as I can tell the gromacs 4 pull code, while very nicely
> enhanced from gromacs 3, has also lost some functionality.
> 
> I am calculating the PMF of a peptide across a bilayer and, to  
> simplify the issue, what I can't figure out how to do with gromacs 4  
> is to pull group1 to a position 1 nm more negative along the z-axis  
> than group 0 (the bilayer in this case) for some replicas and to 1 nm  
> more positive along the z-axis than group 0 in others. I'll focus on  
> the negative displacement here as it is the one that is giving me  
> problems.
> 
> This used to be possible with the following gromacs 3 pull.ppa options:
> 
> runtype   = umbrella
> reftype   = com
> pulldim   = N N Y
> reference_group = group0
> group_1   = group1
> K1= 500
> Pos1  = 0 0 -1.0
> 
> Sure, I could start group1 in the correct negative-z displacement from
> group0 and use pull_init1=+1.0, but this will not work when, for
> instance, I want to restrain it to -0.1 nm (using pull_init1=+0.1),
> where the sampling will infrequently jump back and forth about z=0.
> 
> Just to be sure, I tried for gromacs 4 are the following pull code  
> .mdp options:
> 
> pull = umbrella
> pull_geometry= distance
> pull_dim = N N Y
> pull_start   = no
> pull_ngroups = 1
> pull_group0  = group0
> pull_group1  = group1
> pull_init1   = -1.0
> pull_rate1   = 0
> pull_k1  = 500.0
> 
> where mdrun complains:
> "Pull reference distance for group 1 is negative (-1.00)"
> 
> and it is pretty obvious why this doesn't work since it is asking for
> a negative displacement. Nevertheless, I tried it and pull_init1
> appears to get set to zero.
> 
> I also attempted the following.
> 
> pull = umbrella
> pull_geometry= distance
> pull_dim = N N Y
> pull_start   = no
> pull_ngroups = 1
> pull_group0  = group0
> pull_group1  = group1
> pull_init1   = 1.0
> pull_rate1   = 0
> pull_k1  = 500.0
> pull_vec1= 0 0 -1
> 
> where I would then use
> pull_init1 = 1.0
> pull_vec1  = 0 0 1
> for the positive side of the bilayer.
> 
> However, when I look at the forces, I am getting the negative of what  
> I should get when pull_vec1 = 0 0 -1.
> 
> coord.xvg:
> 610.  4.9343  -1.02019
> 660.0001  4.91454 -0.949747
> 
> force.xvg:
> 610.  -10.0932
> 660.0001  25.1265
> 
> Although I am getting exactly what I should get when pull_vec1 = 0 0 1  
> (for intended positive displacements).
> 
> coord.xvg:
> 660.0001  4.9014  1.16304
> 
> force.xvg:
> 660.0001  -81.5201
> 
> Any ideas are greatly appreciated. I can probably mod the code for my
> needs, but a standard gromacs binary is always preferable.
> 
> Thank you,
> Chris.
> 
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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[gmx-users] pull code with defined negative relative displacements

2009-11-14 Thread chris . neale


Hello, I am re-running some of our gromacs 3 simulations using gromacs
4, and as far as I can tell the gromacs 4 pull code, while very nicely
enhanced from gromacs 3, has also lost some functionality.

I am calculating the PMF of a peptide across a bilayer and, to  
simplify the issue, what I can't figure out how to do with gromacs 4  
is to pull group1 to a position 1 nm more negative along the z-axis  
than group 0 (the bilayer in this case) for some replicas and to 1 nm  
more positive along the z-axis than group 0 in others. I'll focus on  
the negative displacement here as it is the one that is giving me  
problems.


This used to be possible with the following gromacs 3 pull.ppa options:

runtype   = umbrella
reftype   = com
pulldim   = N N Y
reference_group = group0
group_1   = group1
K1= 500
Pos1  = 0 0 -1.0

Sure, I could start group1 in the correct negative-z displacement from
group0 and use pull_init1=+1.0, but this will not work when, for
instance, I want to restrain it to -0.1 nm (using pull_init1=+0.1),
where the sampling will infrequently jump back and forth about z=0.

Just to be sure, I tried for gromacs 4 are the following pull code  
.mdp options:


pull = umbrella
pull_geometry= distance
pull_dim = N N Y
pull_start   = no
pull_ngroups = 1
pull_group0  = group0
pull_group1  = group1
pull_init1   = -1.0
pull_rate1   = 0
pull_k1  = 500.0

where mdrun complains:
"Pull reference distance for group 1 is negative (-1.00)"

and it is pretty obvious why this doesn't work since it is asking for
a negative displacement. Nevertheless, I tried it and pull_init1
appears to get set to zero.

I also attempted the following.

pull = umbrella
pull_geometry= distance
pull_dim = N N Y
pull_start   = no
pull_ngroups = 1
pull_group0  = group0
pull_group1  = group1
pull_init1   = 1.0
pull_rate1   = 0
pull_k1  = 500.0
pull_vec1= 0 0 -1

where I would then use
pull_init1 = 1.0
pull_vec1  = 0 0 1
for the positive side of the bilayer.

However, when I look at the forces, I am getting the negative of what  
I should get when pull_vec1 = 0 0 -1.


coord.xvg:
610.4.9343  -1.02019
660.00014.91454 -0.949747

force.xvg:
610.-10.0932
660.000125.1265

Although I am getting exactly what I should get when pull_vec1 = 0 0 1  
(for intended positive displacements).


coord.xvg:
660.00014.9014  1.16304

force.xvg:
660.0001-81.5201

Any ideas are greatly appreciated. I can probably mod the code for my
needs, but a standard gromacs binary is always preferable.

Thank you,
Chris.



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RE: Re : [gmx-users] PULL CODE AND NpT ensemble

2009-08-27 Thread Berk Hess


Hi,

There are no settings that matter in particular for pulling compared to a 
normal simulation.
All the settings that matter normally matter here as well.
NVT pulling should give nearly identical results no NPT,
as long as you set the volume correctly.

Berk

To: gmx-users@gromacs.org
Subject: Re : [gmx-users] PULL CODE AND NpT ensemble
Date: Thu, 27 Aug 2009 08:03:56 -0400
From: gigita...@aol.fr


 Hi Berk,

Thanks for your answer. I just want to be sure that the procedure is correct. 
No I do not look at the pressure/volume fluctutation. But I do want to make a 
clever choice of the ensemble so that no significant extra artifact are 
generated, since the number of contraint to be calculated is not negligible. I 
previously used no P coupling and I was wondering is that feature could explain 
that the average force plot is not smooth function. Other criteria such as 
Cut-off value for LJ and coulomb may also be checked out?

Geraldine  



 



 


-E-mail d'origine-

De : Berk Hess 

A : Discussion list for GROMACS users 

Envoyé le : Jeudi, 27 Août 2009 13:45

Sujet : RE: [gmx-users] PULL CODE AND NpT ensemble















Hi,



I would use v-rescale and Berendsen pressure coupling.

Although Berendsen pressure coupling, strictly speaking, does not give the 
correct ensemble,

in practice it produces negligible artifacts, unless you are looking at 
pressure/volume fluctuations.



Berk



To: gmx-users@gromacs.org

Date: Thu, 27 Aug 2009 07:20:00 -040
0

From: gigita...@aol.fr

Subject: [gmx-users] PULL CODE AND NpT ensemble



Hi all,


I would like to use pull code to evaluate the free energy of pulling system1 
from system2. Free energy calculation should be done for NpT ensemble. All 
tutorials found for calculating free energy used 


1) berensen for T and P coupling or 


2) berensen for T coupling AND Parrinelo for P coupling or


3)Vrescale for T and no P coupling





I am a bit lost in which one should lead to real ensemble.


Is any one could help?


Regards,


geraldine, phD  




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Re : [gmx-users] PULL CODE AND NpT ensemble

2009-08-27 Thread gigitang5


 Hi Berk,
Thanks for your answer. I just want to be sure that the procedure is correct. 
No I do not look at the pressure/volume fluctutation. But I do want to make a 
clever choice of the ensemble so that no significant extra artifact are 
generated, since the number of contraint to be calculated is not negligible. I 
previously used no P coupling and I was wondering is that feature could explain 
that the average force plot is not smooth function. Other criteria such as 
Cut-off value for LJ and coulomb may also be checked out?
Geraldine  


 


 

-E-mail d'origine-
De : Berk Hess 
A : Discussion list for GROMACS users 
Envoyé le : Jeudi, 27 Août 2009 13:45
Sujet : RE: [gmx-users] PULL CODE AND NpT ensemble













Hi,

I would use v-rescale and Berendsen pressure coupling.
Although Berendsen pressure coupling, strictly speaking, does not give the 
correct ensemble,
in practice it produces negligible artifacts, unless you are looking at 
pressure/volume fluctuations.

Berk



To: gmx-users@gromacs.org
Date: Thu, 27 Aug 2009 07:20:00 -0400
From: gigita...@aol.fr
Subject: [gmx-users] PULL CODE AND NpT ensemble

Hi all,

I would like to use pull code to evaluate the free energy of pulling system1 
from system2. Free energy calculation should be done for NpT ensemble. All 
tutorials found for calculating free energy used 

1) berensen for T and P coupling or 

2) berensen for T coupling AND Parrinelo for P coupling or


3)Vrescale for T and no P coupling



I am a bit lost in which one should lead to real ensemble.

Is any one could help?

Regards,

geraldine, phD  




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RE: [gmx-users] PULL CODE AND NpT ensemble

2009-08-27 Thread Berk Hess


Hi,

I would use v-rescale and Berendsen pressure coupling.
Although Berendsen pressure coupling, strictly speaking, does not give the 
correct ensemble,
in practice it produces negligible artifacts, unless you are looking at 
pressure/volume fluctuations.

Berk

To: gmx-users@gromacs.org
Date: Thu, 27 Aug 2009 07:20:00 -0400
From: gigita...@aol.fr
Subject: [gmx-users] PULL CODE AND NpT ensemble

Hi all,

I would like to use pull code to evaluate the free energy of pulling system1 
from system2. Free energy calculation should be done for NpT ensemble. All 
tutorials found for calculating free energy used 

1) berensen for T and P coupling or 

2) berensen for T coupling AND Parrinelo for P coupling or

3)Vrescale for T and no P coupling



I am a bit lost in which one should lead to real ensemble.

Is any one could help?

Regards,

geraldine, phD  


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[gmx-users] PULL CODE AND NpT ensemble

2009-08-27 Thread gigitang5

Hi all,
I would like to use pull code to evaluate the free energy of pulling system1 
from system2. Free energy calculation should be done for NpT ensemble. All 
tutorials found for calculating free energy used 
1) berensen for T and P coupling or 
2) berensen for T coupling AND Parrinelo for P coupling or
3)Vrescale for T and no P coupling

I am a bit lost in which one should lead to real ensemble.
Is any one could help?
Regards,
geraldine, phD? 
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RE: [gmx-users] pull code problem

2009-08-06 Thread Berk Hess


Hi,

First, please switch to 4.0.5, I have put several fixes in the pull code
in the 4.0 minor releases.

You did not specify pull_init1, nor pull_start, this means you start pulling 
at a distance of 0, which means the center of the bilayer.
Setting
pull_start = yes
should fix your problem.

Berk

Date: Thu, 6 Aug 2009 10:49:26 +0800
From: djpit...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] pull code problem

Hi, all:
I tried to pull a specific DPPC, say, r3, out of a pre-equilibrated bilayer 
into the water along the positive z axis. For the pull code parameters, I used:

pull   = umbrella
pull_geometry= distance
pull_vec1   = 0. 0. 1.
pull_dim= N N Y
pull_nstxout  = 1000
pull_group0   = bilayer
pull_group1   = r3_P

pull_k1 = 500
pull_rate1 = 0.001;nm/ps
integrator  = md
dt = 0.002 ;ps
nsteps  = 100
nstcomm  = 1
comm_grps   = DPP SOL

nstxtcout   = 100
nstlist = 10 
ns_type = grid
pbc = xyz
rlist   = 1.0
coulombtype = PME
rcoulomb= 1.0

vdwtype = cut-off
rvdw= 1.0
ewald_rtol  = 1e-5
optimize_fft= yes
tcoupl  = Berendsen
tau_t   = 0.10.1
tc_grps = DPPSOL

ref_t   = 323323
pcoupl  = Berendsen
pcoupltype  = semiisotropic
tau_p   = 1.0 1.0 
compressibility = 4.5e-5 4.5e-5
ref_p   = 1.0 1.0   

gen_vel = no
gen_temp= 323
gen_seed= 173529
constraints = all-bonds
constraint_algorithm= LINCS
lincs_order = 4

"r3_P" corresponds to an index file that contains the phophorus group of r3, 
and "bilayer" corresponds to an index file that contains all the lipids except 
r3.


I'm using GROMACS 4.0.3, but when I looked at the trajectory in VMD, the 
position of r3 is hardly moved. So what's the right way to pull this specific 
lipid into the water slab?

Thanks.

dj
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[gmx-users] pull code problem

2009-08-05 Thread Jian Dai

Hi, all:
I tried to pull a specific DPPC, say, r3, out of a pre-equilibrated bilayer
into the water along the positive z axis. For the pull code parameters, I
used:
pull   = umbrella
pull_geometry= distance
pull_vec1   = 0. 0. 1.
pull_dim= N N Y
pull_nstxout  = 1000
pull_group0   = bilayer
pull_group1   = r3_P
pull_k1 = 500
pull_rate1 = 0.001;nm/ps
integrator  = md
dt = 0.002 ;ps
nsteps  = 100
nstcomm  = 1
comm_grps   = DPP SOL
nstxtcout   = 100
nstlist = 10
ns_type = grid
pbc = xyz
rlist   = 1.0
coulombtype = PME
rcoulomb= 1.0
vdwtype = cut-off
rvdw= 1.0
ewald_rtol  = 1e-5
optimize_fft= yes
tcoupl  = Berendsen
tau_t   = 0.10.1
tc_grps = DPPSOL
ref_t   = 323323
pcoupl  = Berendsen
pcoupltype  = semiisotropic
tau_p   = 1.0 1.0
compressibility = 4.5e-5 4.5e-5
ref_p   = 1.0 1.0
gen_vel = no
gen_temp= 323
gen_seed= 173529
constraints = all-bonds
constraint_algorithm= LINCS
lincs_order = 4

"r3_P" corresponds to an index file that contains the phophorus group of r3,
and "bilayer" corresponds to an index file that contains all the lipids
except r3.

I'm using GROMACS 4.0.3, but when I looked at the trajectory in VMD, the
position of r3 is hardly moved. So what's the right way to pull this
specific lipid into the water slab?

Thanks.

dj
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[gmx-users] pull code problem solved..

2009-05-11 Thread Andrei Neamtu

Sorry it appears that something was wrong with my .mdp file .. Idon't
know what ...but I wrote again the pull code lines and the warnings
dissapeared.

Thank you again,
Andrei
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RE: [gmx-users] pull code problem

2009-05-11 Thread Berk Hess


Hi,

Maybe there is an older grompp in your path.
Type grompp -h to see which version you are using.
And:
which grompp
to see where it comes from.

Berk

> Date: Mon, 11 May 2009 13:03:07 +0300
> From: neamtuand...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] pull code problem
> 
> Hi Berk,
> thank you for the reply
> 
> here is my mdp file:
> 
> ;
> 
> ; User aneamtu
> 
> ; Joi, 7 mai - 2009
> 
> ; Input file
> 
> ;
> 
> title  =  Production_runs
> 
> ;define =  -DPOSRES -DPOSRES_CA2+_IONS
> 
> 
> 
> ;constraints   =  all-bonds
> 
> 
> 
> integrator =  md
> 
> dt =  0.001   
> 
> nsteps =  5   
> 
> 
> 
> nstcomm=  1
> 
> nstxout=  1000
> 
> nstvout=  1000
> 
> nstfout=  1000
> 
> nstlog =  500
> nstxtcout  =  50
> xtc_grps   =  Protein_ions
> 
> 
> nstenergy  =  100
> 
> nstlist=  10
> 
> ns_type=  grid
> 
> 
> coulombtype=  PME
> 
> rlist  =  1.0
> 
> rcoulomb   =  1.0
> 
> rvdw   =  1.0
> optimize_fft   =  yes
> 
> 
> Tcoupl =  v-rescale
> 
> tc-grps  =  Protein   SOL   ions
> 
> tau_t  =  0.1   0.1   0.1
> 
> ref_t  =  310   310   310
> 
> 
> 
> energygrps =  Protein  SOL CA2+ NA+ CL-
> 
> 
> 
> Pcoupl =  berendsen
> 
> Pcoupltype =  isotropic
> 
> tau_p  =  0.5
> 
> compressibility=  4.5e-5
> 
> ref_p  =  1.0
> 
> 
> 
> gen_vel=  no
> 
> gen_temp   =  310.0
> 
> gen_seed   =  173529
> 
> 
> 
> pull   =  constraint
> pull_geometry  =  distance
> pull_dim   =  Y Y Y
> pull_nstxout   =  10
> pull_nstfout   =  10
> pull_ngroups   =  2
> pull_group0=  Protein
> 
> pull_group1=  CA2+1
> pull_rate1 =  0.3
> 
> pull_group2=  CA2+2
> pull_rate2 =  0.3
> 
> 
> I do not understand what I do wrong..
> Should I use a -pi pull.ppa file like in gromacs 3.x ?
> 
> Andrei
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[gmx-users] pull code problem

2009-05-11 Thread Andrei Neamtu

Hi Berk,
thank you for the reply

here is my mdp file:

;

;   User aneamtu

;   Joi, 7 mai - 2009

;   Input file

;

title  =  Production_runs

;define =  -DPOSRES -DPOSRES_CA2+_IONS



;constraints   =  all-bonds



integrator =  md

dt =  0.001 

nsteps =  5 



nstcomm=  1

nstxout=  1000

nstvout=  1000

nstfout=  1000

nstlog =  500
nstxtcout  =  50
xtc_grps   =  Protein_ions


nstenergy  =  100

nstlist=  10

ns_type=  grid


coulombtype=  PME

rlist  =  1.0

rcoulomb   =  1.0

rvdw   =  1.0
optimize_fft   =  yes


Tcoupl =  v-rescale

tc-grps=  Protein   SOL   ions

tau_t  =  0.1   0.1   0.1

ref_t  =  310   310   310



energygrps =  Protein  SOL CA2+ NA+ CL-



Pcoupl =  berendsen

Pcoupltype =  isotropic

tau_p  =  0.5

compressibility=  4.5e-5

ref_p  =  1.0



gen_vel=  no

gen_temp   =  310.0

gen_seed   =  173529



pull   =  constraint
pull_geometry  =  distance
pull_dim   =  Y Y Y
pull_nstxout   =  10
pull_nstfout   =  10
pull_ngroups   =  2
pull_group0=  Protein

pull_group1=  CA2+1
pull_rate1 =  0.3

pull_group2=  CA2+2
pull_rate2 =  0.3


I do not understand what I do wrong..
Should I use a -pi pull.ppa file like in gromacs 3.x ?

Andrei
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RE: [gmx-users] pull code problem

2009-05-11 Thread Berk Hess


Hi,

Do you have another line with "pull =" somewhere in your mdp file?

PS You should switch to Gromacs 4.0.4, since it contains several small
bug fixes for the pull code.

Berk

> Date: Mon, 11 May 2009 12:38:35 +0300
> From: neamtuand...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] pull code problem
> 
> hello,
> 
> I am trying to do a pulling simulation with gromacs 4.0.2
> 
> I added the following lines to the  .mdp input file for grompp:
> 
> ...
> 
> pull   =  constraint
> pull_geometry  =  distance
> pull_dim   =  Y Y Y
> pull_nstxout   =  10
> pull_nstfout   =  10
> pull_ngroups   =  2
> pull_group0=  Protein
> 
> pull_group1=  CA2+1
> pull_rate1 =  0.3
> 
> pull_group2=  CA2+2
> pull_rate2 =  0.3
> 
> .
> 
> when I run
> > grompp -f production_prm.mdp ...etc.
> 
> it does not recognize the keywords for pulling:
> 
> Ignoring obsolete mdp entry 'title'
> 
> Back Off! I just backed up neutr_RCK_Mthk_solv.04.mdout.mdp to
> ./#neutr_RCK_Mthk_solv.04.mdout.mdp.6#
> 
> WARNING 1 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_geometry' in parameter file
> 
> WARNING 2 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_dim' in parameter file
> 
> WARNING 3 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_nstxout' in parameter file
> 
> WARNING 4 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_nstfout' in parameter file
> 
> WARNING 5 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_ngroups' in parameter file
> 
> WARNING 6 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_group0' in parameter file
> 
> WARNING 7 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_group1' in parameter file
> 
> WARNING 8 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_rate1' in parameter file
> 
> WARNING 9 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_group2' in parameter file
> 
> WARNING 10 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_rate2' in parameter file
> 
> ...
> 
> It appears that grompp doesnot recognize any of these keywords...
> 
> Does anybody can help?
> 
> Thank you
> Andrei
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[gmx-users] pull code problem

2009-05-11 Thread Andrei Neamtu

hello,

I am trying to do a pulling simulation with gromacs 4.0.2

I added the following lines to the  .mdp input file for grompp:

...

pull   =  constraint
pull_geometry  =  distance
pull_dim   =  Y Y Y
pull_nstxout   =  10
pull_nstfout   =  10
pull_ngroups   =  2
pull_group0=  Protein

pull_group1=  CA2+1
pull_rate1 =  0.3

pull_group2=  CA2+2
pull_rate2 =  0.3

.

when I run
> grompp -f production_prm.mdp ...etc.

it does not recognize the keywords for pulling:

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up neutr_RCK_Mthk_solv.04.mdout.mdp to
./#neutr_RCK_Mthk_solv.04.mdout.mdp.6#

WARNING 1 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_geometry' in parameter file

WARNING 2 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_dim' in parameter file

WARNING 3 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_nstxout' in parameter file

WARNING 4 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_nstfout' in parameter file

WARNING 5 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_ngroups' in parameter file

WARNING 6 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_group0' in parameter file

WARNING 7 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_group1' in parameter file

WARNING 8 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_rate1' in parameter file

WARNING 9 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_group2' in parameter file

WARNING 10 [file production_prm.mdp, line unknown]:
  Unknown or double left-hand 'pull_rate2' in parameter file

...

It appears that grompp doesnot recognize any of these keywords...

Does anybody can help?

Thank you
Andrei
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[gmx-users] pull code absolute reference artifacts

2009-04-17 Thread chris . neale


Thanks for the explanation Berk,

I am simply trying to do some tests to ensure that the pull code and  
free energy code are working properly in combination. For this I tried  
to simplify my 'problem' and apply double-decoupling to a solute in a  
box of water under 2 conditions: 1) no pull code, and 2) pull code  
with an absolute reference to pin the decoupled molecule in place  
harmonically. Since the water box is isotropic, I should get the same  
overall free energy for decoupling (which I do in spite of the warning  
message, perhaps because I don't change the reference position over  
time).


Thanks again,
Chris.

-- original message --

Hi,

I have no clue why you would want to fix the peptide in the middle of the box.
But what you want seems to be more like com removal for the peptide only
with the comm options.
The pull code will do approximately what you want, but with pressure coupling
there is the problem that your peptide will stay fixed in space, while  
the rest

of the system has to scale around it.

In general there are problems with absolute reference pulling, because  
you just
fix the location of the pull group, whereas the rest of the system can  
freely move,
thus the net effect is zero, except for lots of nasty artifacts when  
you change

the pull position too fast.

Berk


Date: Thu, 16 Apr 2009 10:27:04 -0400
From: chris.neale at utoronto.ca
To: gmx-users at gromacs.org
Subject: [gmx-users] pull code absolute reference artifacts

Hello,

I have a question about the following grompp 4.0.4 warning:

"You are using an absolute reference for pulling, but the rest of  
the  system does not have an absolute reference. This will lead to   
artifacts."


While I do realize that this is an excellent error message  
containing  lots of information, I am still unclear about how to  
proceed. Why does  my system not have an absolute reference? Is it  
because I have pbc and  center of mass motion removal? Exactly what  
types of artifacts are  expected? Is there a simple solution?


I am trying to hold my peptide in the center of a water box. I  
realize  that there is no "center" and everything in pbc, but I need  
to do it  nevertheless.


Here are my .mdp options:

pull= umbrella
pull_geometry   = distance
pull_dim= Y Y Y
pull_ngroups= 1
;pull_group0 =
pull_group1 = peptide_A
pull_k1 = 500
pull_init1  = 0.00

nsteps  =  25 ; REMOVE_FOR_EM
tinit   =  49000  ; REMOVE_FOR_EM
dt  =  0.004  ; REMOVE_FOR_EM
nstxout =  25 ; REMOVE_FOR_EM
nstvout =  25 ; REMOVE_FOR_EM
nstfout =  25 ; REMOVE_FOR_EM
nstenergy   =  25000 ; REMOVE_FOR_EM
nstxtcout   =  25000 ; REMOVE_FOR_EM
nstlog  =  25; REMOVE_FOR_EM
gen_vel =  no
unconstrained-start =  yes

integrator  =  sd
gen_seed=  -1
comm_mode   =  linear
nstcomm =  1
comm_grps   =  System
nstlist =  5
ns_type =  grid
pbc =  xyz
coulombtype =  PME
rcoulomb=  0.9
fourierspacing  =  0.12
pme_order   =  4
vdwtype =  cut-off
rvdw_switch =  0
rvdw=  1.4
rlist   =  0.9
DispCorr=  EnerPres
Pcoupl  =  Berendsen  ; REMOVE_FOR_EM
pcoupltype  =  isotropic  ; REMOVE_FOR_EM
compressibility =  4.5e-5 ; REMOVE_FOR_EM
ref_p   =  1. ; REMOVE_FOR_EM
tau_p   =  4.0; REMOVE_FOR_EM
tc_grps =  System ; REMOVE_FOR_EM
tau_t   =  1.0; REMOVE_FOR_EM
ld_seed =  -1 ; REMOVE_FOR_EM
ref_t   =  300.   ; REMOVE_FOR_EM
gen_temp=  300.   ; REMOVE_FOR_EM
constraints =  all-bonds  ; REMOVE_FOR_EM
constraint_algorithm=  lincs  ; REMOVE_FOR_EM
lincs-iter  =  1  ; REMOVE_FOR_EM
lincs-order =  6  ; REMOVE_FOR_EM


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-- next part ---

RE: [gmx-users] pull code absolute reference artifacts

2009-04-17 Thread Berk Hess


Hi,

I have no clue why you would want to fix the peptide in the middle of the box.
But what you want seems to be more like com removal for the peptide only
with the comm options.
The pull code will do approximately what you want, but with pressure coupling
there is the problem that your peptide will stay fixed in space, while the rest
of the system has to scale around it.

In general there are problems with absolute reference pulling, because you just
fix the location of the pull group, whereas the rest of the system can freely 
move,
thus the net effect is zero, except for lots of nasty artifacts when you change
the pull position too fast.

Berk

> Date: Thu, 16 Apr 2009 10:27:04 -0400
> From: chris.ne...@utoronto.ca
> To: gmx-users@gromacs.org
> Subject: [gmx-users] pull code absolute reference artifacts
> 
> Hello,
> 
> I have a question about the following grompp 4.0.4 warning:
> 
> "You are using an absolute reference for pulling, but the rest of the  
> system does not have an absolute reference. This will lead to  
> artifacts."
> 
> While I do realize that this is an excellent error message containing  
> lots of information, I am still unclear about how to proceed. Why does  
> my system not have an absolute reference? Is it because I have pbc and  
> center of mass motion removal? Exactly what types of artifacts are  
> expected? Is there a simple solution?
> 
> I am trying to hold my peptide in the center of a water box. I realize  
> that there is no "center" and everything in pbc, but I need to do it  
> nevertheless.
> 
> Here are my .mdp options:
> 
> pull= umbrella
> pull_geometry   = distance
> pull_dim= Y Y Y
> pull_ngroups= 1
> ;pull_group0 =
> pull_group1 = peptide_A
> pull_k1 = 500
> pull_init1  = 0.00
> 
> nsteps  =  25 ; REMOVE_FOR_EM
> tinit   =  49000  ; REMOVE_FOR_EM
> dt  =  0.004  ; REMOVE_FOR_EM
> nstxout =  25 ; REMOVE_FOR_EM
> nstvout =  25 ; REMOVE_FOR_EM
> nstfout =  25 ; REMOVE_FOR_EM
> nstenergy   =  25000 ; REMOVE_FOR_EM
> nstxtcout   =  25000 ; REMOVE_FOR_EM
> nstlog  =  25; REMOVE_FOR_EM
> gen_vel =  no
> unconstrained-start =  yes
> 
> integrator  =  sd
> gen_seed=  -1
> comm_mode   =  linear
> nstcomm =  1
> comm_grps   =  System
> nstlist =  5
> ns_type =  grid
> pbc =  xyz
> coulombtype =  PME
> rcoulomb=  0.9
> fourierspacing  =  0.12
> pme_order   =  4
> vdwtype =  cut-off
> rvdw_switch =  0
> rvdw=  1.4
> rlist   =  0.9
> DispCorr=  EnerPres
> Pcoupl  =  Berendsen  ; REMOVE_FOR_EM
> pcoupltype  =  isotropic  ; REMOVE_FOR_EM
> compressibility =  4.5e-5 ; REMOVE_FOR_EM
> ref_p   =  1. ; REMOVE_FOR_EM
> tau_p   =  4.0; REMOVE_FOR_EM
> tc_grps =  System ; REMOVE_FOR_EM
> tau_t   =  1.0; REMOVE_FOR_EM
> ld_seed =  -1 ; REMOVE_FOR_EM
> ref_t   =  300.   ; REMOVE_FOR_EM
> gen_temp=  300.   ; REMOVE_FOR_EM
> constraints =  all-bonds  ; REMOVE_FOR_EM
> constraint_algorithm=  lincs  ; REMOVE_FOR_EM
> lincs-iter  =  1  ; REMOVE_FOR_EM
> lincs-order =  6  ; REMOVE_FOR_EM
> 
> 
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Re: [gmx-users] pull code absolute reference artifacts

2009-04-16 Thread rversace

Hi Justin:

1) EXTREMELY IMPORTANT: I already know of 1 person, but is anyone alergic to 
either Iodine or Chlorine?
No, I am not alergic to those compounds. The only thing that I am alergic is 
Penicillin and Ampicilin.  

2) Any other medical problems?
No
 
3) An Emergency contact person.
Fernando Babilonia. 
Telf: 646 752 6557
  
4) What food are you planning on bringing? If anyone is planning on bringing 
food that needs to be heated, cooked, or boiled i need to re-calculate how much 
fuel we need for the stove incase the rain prevents us from lighting a fire.

I am planning to take fast easy food like tuna or sandwiches. The only thing 
that i am planning to use heat is to boil water for instant tea and also I 
planning to have some hotdogs at dinner.

-Rodney 
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[gmx-users] pull code absolute reference artifacts

2009-04-16 Thread chris . neale


Hello,

I have a question about the following grompp 4.0.4 warning:

"You are using an absolute reference for pulling, but the rest of the  
system does not have an absolute reference. This will lead to  
artifacts."


While I do realize that this is an excellent error message containing  
lots of information, I am still unclear about how to proceed. Why does  
my system not have an absolute reference? Is it because I have pbc and  
center of mass motion removal? Exactly what types of artifacts are  
expected? Is there a simple solution?


I am trying to hold my peptide in the center of a water box. I realize  
that there is no "center" and everything in pbc, but I need to do it  
nevertheless.


Here are my .mdp options:

pull= umbrella
pull_geometry   = distance
pull_dim= Y Y Y
pull_ngroups= 1
;pull_group0 =
pull_group1 = peptide_A
pull_k1 = 500
pull_init1  = 0.00

nsteps  =  25 ; REMOVE_FOR_EM
tinit   =  49000  ; REMOVE_FOR_EM
dt  =  0.004  ; REMOVE_FOR_EM
nstxout =  25 ; REMOVE_FOR_EM
nstvout =  25 ; REMOVE_FOR_EM
nstfout =  25 ; REMOVE_FOR_EM
nstenergy   =  25000 ; REMOVE_FOR_EM
nstxtcout   =  25000 ; REMOVE_FOR_EM
nstlog  =  25; REMOVE_FOR_EM
gen_vel =  no
unconstrained-start =  yes

integrator  =  sd
gen_seed=  -1
comm_mode   =  linear
nstcomm =  1
comm_grps   =  System
nstlist =  5
ns_type =  grid
pbc =  xyz
coulombtype =  PME
rcoulomb=  0.9
fourierspacing  =  0.12
pme_order   =  4
vdwtype =  cut-off
rvdw_switch =  0
rvdw=  1.4
rlist   =  0.9
DispCorr=  EnerPres
Pcoupl  =  Berendsen  ; REMOVE_FOR_EM
pcoupltype  =  isotropic  ; REMOVE_FOR_EM
compressibility =  4.5e-5 ; REMOVE_FOR_EM
ref_p   =  1. ; REMOVE_FOR_EM
tau_p   =  4.0; REMOVE_FOR_EM
tc_grps =  System ; REMOVE_FOR_EM
tau_t   =  1.0; REMOVE_FOR_EM
ld_seed =  -1 ; REMOVE_FOR_EM
ref_t   =  300.   ; REMOVE_FOR_EM
gen_temp=  300.   ; REMOVE_FOR_EM
constraints =  all-bonds  ; REMOVE_FOR_EM
constraint_algorithm=  lincs  ; REMOVE_FOR_EM
lincs-iter  =  1  ; REMOVE_FOR_EM
lincs-order =  6  ; REMOVE_FOR_EM


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Re: [gmx-users] Pull code using two reaction coordinates??

2009-03-16 Thread XAvier Periole



Hi Rodney,

the other alternative is to define the springs in your topology file.  
You first need to merge
your groups (is part of different molecules) and run the different  
combination you need by
defining them by hand; you can easily write a awk script to generate  
the different topologies

you need.
Then you can use a 2D wham to combine the different histograms you've  
obtained and

get your 2D PMF.

XAvier.

On Mar 16, 2009, at 8:28 PM,  > wrote:



Hello everybody:
I am trying to perform some PMF calculations using the pull code  
with a spring (umbrella sampling) but using two reaction coordinates  
(E1 and E2) between four different groups (r1,r2,r3 and r4).
All the examples and tutorials that I found so far on the web, only  
mention PMF calculations for one reaction coordinate (E1) between  
two different groups (r1 and r2).
Is it possible to perform the calculations using two reaction  
coordinates at the same time or should i do two different individual  
calculations or there is something more that i should do to achieve  
it?

I will appreciate any help.
-Rodney

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[gmx-users] Pull code using two reaction coordinates??

2009-03-16 Thread Chris Neale

Hi Rodney,

This may be possible if your reference is absolute coordinates. In this case, just use pull group 1 and 2, with the
reference group undefined. For more nuanced usage, the problem is that you are only allowed one
reference group (and one type of pull code usage) in a given run.

I put a request for this type of functionality on the wiki wish list a long
time ago and it never materialized, so my best
guess is that it will not be done in the near future.

Quoting http://wiki.gromacs.org/index.php/Development:
"* The ability to read in multiple .ppa files, for example to allow one pull-code implementation of an umbrella in
absolute coordinates and one relative to a reference group, or one umbrella and one constraint and one afm, etc.
* Since the pull code is now integrated into the mdp file in gromacs 4, this request now has a different format,
but the functionality requested remains the same."

You might be able to do something with special "bonds" if you can't use an
absolute reference.

Chris.

-- original message --

Hello everybody:
I am trying to perform some PMF calculations using the pull code with a spring (umbrella sampling) but using two reaction coordinates (E1 and E2) between four different groups (r1,r2,r3 and r4).
All the examples and tutorials that I found so far on the web, only mention PMF calculations for one reaction coordinate (E1) between two different groups (r1 and r2).
Is it possible to perform the calculations using two reaction coordinates at the same time or should i do two different individual calculations or there is something more that i should do to achieve it?

I will appreciate any help.
-Rodney

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[gmx-users] Pull code using two reaction coordinates??

2009-03-16 Thread rversace

Hello everybody:
I am trying to perform some PMF calculations using the pull code with a spring 
(umbrella sampling) but using two reaction coordinates (E1 and E2) between four 
different groups (r1,r2,r3 and r4). 
All the examples and tutorials that I found so far on the web, only mention PMF 
calculations for one reaction coordinate (E1) between two different groups (r1 
and r2). 
Is it possible to perform the calculations using two reaction coordinates at 
the same time or should i do two different individual calculations or there is 
something more that i should do to achieve it?
I will appreciate any help.
-Rodney

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[gmx-users] pull code, lambda, and soft core availability

2009-02-12 Thread chris . neale

Upon further investigation, it appears that a soft core may help in  
this case. This is in spite of the fact that the problem is not a  
singularity, but that the dgdl term (dgdl=0.5*(Fc_B-Fc_A)*(r-r0)^2)  
gives very large values for Fc_A large enough to be significantly  
restraining and Fc_B = zero, where the sampling in the B state is  
massively unlikely to occur in the A state. I had originally thought  
that the lambda parameter would get included in dgdl  
(http://www.gromacs.org/pipermail/gmx-developers/2009-February/003004.html)  
but that is obviously not the case.


I have found an alternative solution, but in case anyone else wants to  
follow this path in the future, it is possible that a lambda squared  
dependence would give improved behaviour since lambda would then be  
included in the dgdl equation. My quite possibly incorrect attempt at  
differentiation yields dgdl=(lambda-0.5)*Fc_A*(r-r0)^2 in this case  
where Fc_B=0.0, but in any event the (1-lambda)^2 term will ensure  
that lambda hangs around in some form, and this should reduce the  
uncertainties that occur near and at the no-restraint state.


Chris.

-- original message --

Thank you Matt, that is indeed the perfect paper. I'll post back here
once I figure out exactly where the (1-lambda)^2 term would fit into
the pull code US equation.

Chris.

This seems to be a good reference for soft-core interactions.

BEUTLER et al. AVOIDING SINGULARITIES AND NUMERICAL INSTABILITIES IN
FREE-ENERGY CALCULATIONS BASED ON MOLECULAR SIMULATIONS. Chem Phys
Lett (1994) vol. 222 pp. 529-539

On Thu, Feb 12, 2009 at 1:33 PM,   wrote:
  Does anybody know of a good paper that

describes the underlying equations that define soft core?

Thanks,
Chris.


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[gmx-users] pull code, lambda, and soft core availability

2009-02-12 Thread chris . neale

Thank you Matt, that is indeed the perfect paper. I'll post back here  
once I figure out exactly where the (1-lambda)^2 term would fit into  
the pull code US equation.


Chris.

This seems to be a good reference for soft-core interactions.

BEUTLER et al. AVOIDING SINGULARITIES AND NUMERICAL INSTABILITIES IN
FREE-ENERGY CALCULATIONS BASED ON MOLECULAR SIMULATIONS. Chem Phys
Lett (1994) vol. 222 pp. 529-539

On Thu, Feb 12, 2009 at 1:33 PM,   wrote:
 Does anybody know of a good paper that

describes the underlying equations that define soft core?

Thanks,
Chris.


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Re: [gmx-users] pull code, lambda, and soft core availability

2009-02-12 Thread Matt Wyczalkowski

This seems to be a good reference for soft-core interactions.

BEUTLER et al. AVOIDING SINGULARITIES AND NUMERICAL INSTABILITIES IN
FREE-ENERGY CALCULATIONS BASED ON MOLECULAR SIMULATIONS. Chem Phys
Lett (1994) vol. 222 pp. 529-539

On Thu, Feb 12, 2009 at 1:33 PM,   wrote:
 Does anybody know of a good paper that
> describes the underlying equations that define soft core?
>
> Thanks,
> Chris.
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[gmx-users] pull code, lambda, and soft core availability

2009-02-12 Thread chris . neale


Hello,

I see from looking at the source code that the free-energy lambda  
dependence is now available to the pull code based on pull_kB1.  
However, this leads to serious problems converging near lambda=1 when  
pull_k1=large and pull_kB1=0 and in the absence of a restraint (with  
k=0) the pulled COM is allowed to sample a large volume. I suspect  
that a soft core lambda dependence would help here, but the  
descriptions in the .mpd options section of the online manual indicate  
that this is available only for Lj and coulombic.


Quoting:
"sc_alpha: (0) the soft-core parameter, a value of 0 results in linear  
interpolation of the LJ and Coulomb interactions"


Does anybody know if it is possible to get soft core potentials for an  
arbitrary coordinate?


I tested the application of this myself by bypassing the free energy  
code and simply modifying the A-state pull_k1 value based on lambda  
0->1 and then calculating dGdl from the px.xvg file myself. However, I  
am unclear how one would implement this as soft core. Does anybody  
know of a good paper that describes the underlying equations that  
define soft core?


Thanks,
Chris.

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Re: [gmx-users] pull code

2009-01-21 Thread Justin A. Lemkul




avinash kumar wrote:

Hello all,

does anybody possess a sample of  "pull.pdo" data file for pull codes.



The pull.pdo file is output, are you sure that's what you want, or do you want a 
pull.ppa input file?  Either way, enter "pull.pdo" or "pull.ppa" into the Search 
page for the archive and you will get tons of hits.


-Justin

--


Justin A. Lemkul
Graduate Research Assistant
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] pull code

2009-01-21 Thread avinash kumar

Hello all,

does anybody possess a sample of  "pull.pdo" data file for pull codes.

-- 
Avinash Kumar.
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[gmx-users] Pull code - 2

2009-01-16 Thread DimitryASuplatov

Hello,

I was running different simulations with the following pull code

1/ 
;---PULL CODE -

pull=   umbrella
pull_geometry   = direction
pull_group1 = r_535
pull_vec1   = 0.51 0.026 0.273
pull_k1 = 110
pull_rate1  = 0.002 ; nm/ps = 20 A/ns
pull_start  = yes
pull_init1  = 0

2/ Different pull group

;---PULL CODE -

pull=   umbrella
pull_geometry   = direction
pull_group1 = r_538
pull_vec1   = 0.51 0.026 0.273
pull_k1 = 110
pull_rate1  = 0.002 ; nm/ps = 20 A/ns
pull_start  = yes
pull_init1  = 0


3/ Two pull groups

;---PULL CODE -

pull=   umbrella
pull_geometry   = direction

pull_ngroups= 2

pull_group1 = r_533
pull_vec1   = 0.51 0.026 0.273
pull_k1 = 110
pull_rate1  = 0.002 ; nm/ps = 10 A/ns
pull_init1  = 0

pull_group2 = r_538
pull_vec2   = 0.51 0.026 0.273
pull_k2 = 110
pull_rate2  = 0.002 ; nm/ps = 20 A/ns
pull_init2  = 0

pull_start  = yes


Additionaly I`ve added the following lines to each file
comm-mode   = angular
nstcomm =  10


I have constructed the pull vector by taking the coordinates of CA of
pull_group and coordinates of OW in a water molecule that was
positioned in the direction I wanted to pull. Finally, I have calculated the
vector by substraction (x2(water) - x1(CA_aminoacid); y2-y1; z2-z1). 

Observing the results of my simulation I have observed two problems:

1/ Groups are pulled not exactly in the same direction differing by about 45 
degrees. I guess that means that system is rotating even though I set comm-mode 
to angular!!!
2/ The first 5 ns I see no indication of pulling and the force is climbing 
evenly. Then I see a huge force leap up followed by a leap down (in some 
picoseconds) corresponding to displacement of pull group.
I just don`t understand why force is growing so fast. 

What am I doing wrong? Any suggestions?
Thank you. I appreciate your time.

SDA

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RE: [gmx-users] Pull Code problems


Hi,

If you pull without a reference, you will be doing nothing in the limit
of slow pulling. For fast pulling you will be doing something.

pull_start=yes
pull_init1=0
will initialize set pull_init to the initial distance.

Berk

> Subject: RE: [gmx-users] Pull Code problems
> From: gene...@gmail.com
> To: gmx-users@gromacs.org
> Date: Tue, 13 Jan 2009 19:59:38 +0300
> 
> OK,
> 
> finally I try to simplify my question by revealing my final aim.
> 
> I have a group that I want to pull out of my protein. I want only one
> group to be pulled out in one direction. 
> 
> How could I do that?
> SDA
> 
> P.S.
> In my understanding to do that I should leave reference group blank and
> specify pull group only:
> pull_group0=
> pull_group1=r_535
> In this case grompp calculates initial distance from (0,0,0) to pull
> group and sets the initial force to a very high value
> (distance*force_constant) instead of 0. To correct this and to make the
> initial pull rate = 0 I should set pull group to the center of
> coordinates or set the initial position of the pull spring to the
> position of the pull group.  How should I do that?
> 
> 
> On Tue, 2009-01-13 at 16:55 +0100, Berk Hess wrote:
> > Hi,
> > 
> > The pull option acts between COM's. Both COM's will move.
> > If not, you would have a net force on the COM of the whole system.
> > 
> > The AFM option is no longer there.
> > I never understood what the difference between Umbrella and AFM was.
> > But Umbrella (as well as constraint) should be able to do all things
> > that were possible before (and more).
> > 
> > Berk
> > 
> > > Subject: Re: [gmx-users] Pull Code problems
> > > From: gene...@gmail.com
> > > To: gmx-users@gromacs.org
> > > Date: Tue, 13 Jan 2009 18:44:36 +0300
> > > 
> > > OK,
> > > I have a new problem.
> > > I`ve started the simulation with the following pull parameters
> > > 
> > > 
> > > ;---PULL CODE -
> > > 
> > > pull<-->=<-> umbrella
> > > pull_geometry<->= direction
> > > pull_group0<-->= r_500
> > > pull_group1<--->= r_535
> > > pull_vec1<->= -1.306 1.355 -0.319
> > > pull_k1><-->= 1000
> > > pull_rate1<>= 1 ; nm/ps = 1 A/ns
> > > 
> > > With such extreme pulling velocities I had my system teared apart in
> > 100
> > > ps - that is OK I suggest. The problem is that pull group
> > (pull_group1)
> > > and reference group (pull_group0) were both pulled in opposite
> > > directions - pull_vec1 and -(pull_vec1)?!
> > > 
> > > 1/ In my best understanding the reference group is the one that
> > stays
> > > intact to track the movement of the group that is being pulled -
> > pull
> > > group. Then how could this happen in my system? What should I do to
> > pull
> > > only the pull_group1?
> > > 2/ I was recomended to use AFM pull mode in gromacs 3. What is the
> > new
> > > name for AFM in gromacs 4? 
> > > 
> > > Thanks.
> > > 
> > > 
> > > ___
> > > gmx-users mailing list gmx-users@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 
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> > 
> > 
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RE: [gmx-users] Pull Code problems

OK,

finally I try to simplify my question by revealing my final aim.

I have a group that I want to pull out of my protein. I want only one
group to be pulled out in one direction. 

How could I do that?
SDA

P.S.
In my understanding to do that I should leave reference group blank and
specify pull group only:
pull_group0=
pull_group1=r_535
In this case grompp calculates initial distance from (0,0,0) to pull
group and sets the initial force to a very high value
(distance*force_constant) instead of 0. To correct this and to make the
initial pull rate = 0 I should set pull group to the center of
coordinates or set the initial position of the pull spring to the
position of the pull group.  How should I do that?

On Tue, 2009-01-13 at 16:55 +0100, Berk Hess wrote:
> Hi,
> 
> The pull option acts between COM's. Both COM's will move.
> If not, you would have a net force on the COM of the whole system.
> 
> The AFM option is no longer there.
> I never understood what the difference between Umbrella and AFM was.
> But Umbrella (as well as constraint) should be able to do all things
> that were possible before (and more).
> 
> Berk
> 
> > Subject: Re: [gmx-users] Pull Code problems
> > From: gene...@gmail.com
> > To: gmx-users@gromacs.org
> > Date: Tue, 13 Jan 2009 18:44:36 +0300
> > 
> > OK,
> > I have a new problem.
> > I`ve started the simulation with the following pull parameters
> > 
> > 
> > ;---PULL CODE -
> > 
> > pull<-->=<-> umbrella
> > pull_geometry<->= direction
> > pull_group0<-->= r_500
> > pull_group1<--->= r_535
> > pull_vec1<->= -1.306 1.355 -0.319
> > pull_k1><-->= 1000
> > pull_rate1<>= 1 ; nm/ps = 1 A/ns
> > 
> > With such extreme pulling velocities I had my system teared apart in
> 100
> > ps - that is OK I suggest. The problem is that pull group
> (pull_group1)
> > and reference group (pull_group0) were both pulled in opposite
> > directions - pull_vec1 and -(pull_vec1)?!
> > 
> > 1/ In my best understanding the reference group is the one that
> stays
> > intact to track the movement of the group that is being pulled -
> pull
> > group. Then how could this happen in my system? What should I do to
> pull
> > only the pull_group1?
> > 2/ I was recomended to use AFM pull mode in gromacs 3. What is the
> new
> > name for AFM in gromacs 4? 
> > 
> > Thanks.
> > 
> > 
> > ___
> > gmx-users mailing list gmx-users@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-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> __
> Express yourself instantly with MSN Messenger! MSN Messenger

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RE: [gmx-users] Pull Code problems


Hi,

The pull option acts between COM's. Both COM's will move.
If not, you would have a net force on the COM of the whole system.

The AFM option is no longer there.
I never understood what the difference between Umbrella and AFM was.
But Umbrella (as well as constraint) should be able to do all things
that were possible before (and more).

Berk

> Subject: Re: [gmx-users] Pull Code problems
> From: gene...@gmail.com
> To: gmx-users@gromacs.org
> Date: Tue, 13 Jan 2009 18:44:36 +0300
> 
> OK,
> I have a new problem.
> I`ve started the simulation with the following pull parameters
> 
> 
> ;---PULL CODE -
> 
> pull<-->=<->  umbrella
> pull_geometry<->= direction
> pull_group0<-->= r_500
> pull_group1<--->= r_535
> pull_vec1<->= -1.306 1.355 -0.319
> pull_k1><-->= 1000
> pull_rate1<>= 1 ; nm/ps = 1 A/ns
> 
> With such extreme pulling velocities I had my system teared apart in 100
> ps - that is OK I suggest. The problem is that pull group (pull_group1)
> and reference group (pull_group0) were both pulled in opposite
> directions - pull_vec1 and -(pull_vec1)?!
> 
> 1/ In my best understanding the reference group is the one that stays
> intact to track the movement of the group that is being pulled - pull
> group. Then how could this happen in my system? What should I do to pull
> only the pull_group1?
> 2/ I was recomended to use AFM pull mode in gromacs 3. What is the new
> name for AFM in gromacs 4? 
> 
> Thanks.
> 
> 
> ___
> gmx-users mailing listgmx-users@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 
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Re: [gmx-users] Pull Code problems

OK,
I have a new problem.
I`ve started the simulation with the following pull parameters


;---PULL CODE -

pull<-->=<->  umbrella
pull_geometry<->= direction
pull_group0<-->= r_500
pull_group1<--->= r_535
pull_vec1<->= -1.306 1.355 -0.319
pull_k1><-->= 1000
pull_rate1<>= 1 ; nm/ps = 1 A/ns

With such extreme pulling velocities I had my system teared apart in 100
ps - that is OK I suggest. The problem is that pull group (pull_group1)
and reference group (pull_group0) were both pulled in opposite
directions - pull_vec1 and -(pull_vec1)?!

1/ In my best understanding the reference group is the one that stays
intact to track the movement of the group that is being pulled - pull
group. Then how could this happen in my system? What should I do to pull
only the pull_group1?
2/ I was recomended to use AFM pull mode in gromacs 3. What is the new
name for AFM in gromacs 4? 

Thanks.


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RE: [gmx-users] Pull Code problems


Hi,

pullx.xvg has the coordinates of group 0 and the distances
of the other groups to group 0.

pullf.xvg has the force of the umbrella potential
which works along the direction vector you gave,
this can be positive or negative depending on the direction.

Berk

> Subject: RE: [gmx-users] Pull Code problems
> From: gene...@gmail.com
> To: gmx-users@gromacs.org
> Date: Tue, 13 Jan 2009 18:02:47 +0300
> 
> OK, 
> I did some homework and now I`m up to this:
> 
> ;---PULL CODE -
> 
> pull=   umbrella
> pull_geometry   = direction
> pull_group0 = r_500
> pull_group1 = r_535
> pull_vec1   = -1.306 1.355 -0.319
> pull_k1 = 1000
> pull_rate1  = 0.5 ; nm/ps Extreme parameters for extreme pulling
> 
> Now I have two output files - pullx.xvg (-px option of mdrun) and
> pullf.xvg (-pf option).
> 
> pullx :
> 
> @title "Pull COM"
> @xaxis  label "Time (ps)"
> @yaxis  label "Position (nm)"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "0 X"
> @ s1 legend "0 Y"
> @ s2 legend "0 Z"
> @ s3 legend "1 dX"
> @ s4 legend "1 dY"
> @ s5 legend "1 dZ"
> 0.003.8995935.8163683.246447
> -0.285972   -0.132647   -0.183023
> 0.043.9011635.8121323.238992
> -0.292108   -0.141616   -0.180796
> 0.083.9025055.8062123.240236
> -0.314770   -0.143951   -0.186194
> 0.123.9053655.7979383.242384
> -0.336802   -0.142276   -0.197704
> 0.163.9088995.7948123.230687
> -0.342824   -0.160593   -0.178745
> 0.203.9101085.7975643.220754
> -0.340151   -0.161146   -0.152076
> 
> Am I correct about XYZ being position of the spring and dx dy dz -
> group0-group1 distances?
> 
> pullf :
> 
> @title "Pull force"
> @xaxis  label "Time (ps)"
> @yaxis  label "Force (kJ/mol/nm)"
> @TYPE xy
> 0.00-132.088161
> 0.004000-128.605515
> 0.008000-125.008520
> 0.012000-121.568624
> 0.016000-118.475655
> 0.02-115.844403
> 0.024000-113.735184
> 0.028000-112.165522
> 0.032000-111.066433
> . ...
> 1.232000409.573773
> 1.236000412.738957
> 1.24415.736038
> 1.244000418.446270
> 1.248000420.781766
> 1.252000422.747570
> 1.256000424.505472
> 1.26426.348269
> 1.264000428.568933
> 1.268000431.301610
> 1.272000434.467394
> 
> Why does it start with negative values? Should I use negative value for
> pull_k1 (force constant)?
> 
> Thank you for your answers, I appreciate your time.
> 
> SDA
> 
> 
> 
> On Tue, 2009-01-13 at 12:41 +0100, Berk Hess wrote:
> > Hi,
> > 
> > You don't indicate which xvg file was 0, I guess pullf.xvg.
> > Could it be that you did not specify a force constant, meaning fc=0?
> > 
> > Berk
> > 
> > > From: gene...@gmail.com
> > > To: gmx-users@gromacs.org
> > > Date: Tue, 13 Jan 2009 14:26:47 +0300
> > > Subject: [gmx-users] Pull Code problems
> > > 
> > > Hello,
> > > 
> > > I am trying to run a pulling simulation with gromacs 4.0.2.
> > > 
> > > I have appended the following pull code to the mdp file:
> > > 
> > > ;---PULL CODE -
> > > 
> > > pull = umbrella
> > > pull_geometry = direction
> > > pull_group0 = r_500
> > > pull_group1 = r_535
> > > pull_vec1 = -1.306 1.355 -0.319
> > > 
> > > Where r_500 is the group I am expecting to be pulled,
> > > r_535 - the reference (the acid that is in fact in contact with
> > > r_500)
> > > 
> > > I have left all remaining parameters with default values. 
> > > 
> > > The problem is that NOTHING HAPPENED! XVG file had 0. throughout
> > > simulation indicating that distance between pull group and reference
> > > group was 0! 
> > > 
> > > 1/ What did I do wrong?
> > > 2/ Is there any pull code tutorial for gromacs 4 (n

RE: [gmx-users] Pull Code problems

OK, 
I did some homework and now I`m up to this:

;---PULL CODE -

pull=   umbrella
pull_geometry   = direction
pull_group0 = r_500
pull_group1 = r_535
pull_vec1   = -1.306 1.355 -0.319
pull_k1 = 1000
pull_rate1  = 0.5 ; nm/ps Extreme parameters for extreme pulling

Now I have two output files - pullx.xvg (-px option of mdrun) and
pullf.xvg (-pf option).

pullx :

@title "Pull COM"
@xaxis  label "Time (ps)"
@yaxis  label "Position (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "0 X"
@ s1 legend "0 Y"
@ s2 legend "0 Z"
@ s3 legend "1 dX"
@ s4 legend "1 dY"
@ s5 legend "1 dZ"
0.003.8995935.8163683.246447
-0.285972   -0.132647   -0.183023
0.043.9011635.8121323.238992
-0.292108   -0.141616   -0.180796
0.083.9025055.8062123.240236
-0.314770   -0.143951   -0.186194
0.123.9053655.7979383.242384
-0.336802   -0.142276   -0.197704
0.163.9088995.7948123.230687
-0.342824   -0.160593   -0.178745
0.203.9101085.7975643.220754
-0.340151   -0.161146   -0.152076

Am I correct about XYZ being position of the spring and dx dy dz -
group0-group1 distances?

pullf :

@title "Pull force"
@xaxis  label "Time (ps)"
@yaxis  label "Force (kJ/mol/nm)"
@TYPE xy
0.00-132.088161
0.004000-128.605515
0.008000-125.008520
0.012000-121.568624
0.016000-118.475655
0.02-115.844403
0.024000-113.735184
0.028000-112.165522
0.032000-111.066433
.   ...
1.232000409.573773
1.236000412.738957
1.24415.736038
1.244000418.446270
1.248000420.781766
1.252000422.747570
1.256000424.505472
1.26426.348269
1.264000428.568933
1.268000431.301610
1.272000434.467394

Why does it start with negative values? Should I use negative value for
pull_k1 (force constant)?

Thank you for your answers, I appreciate your time.

SDA



On Tue, 2009-01-13 at 12:41 +0100, Berk Hess wrote:
> Hi,
> 
> You don't indicate which xvg file was 0, I guess pullf.xvg.
> Could it be that you did not specify a force constant, meaning fc=0?
> 
> Berk
> 
> > From: gene...@gmail.com
> > To: gmx-users@gromacs.org
> > Date: Tue, 13 Jan 2009 14:26:47 +0300
> > Subject: [gmx-users] Pull Code problems
> > 
> > Hello,
> > 
> > I am trying to run a pulling simulation with gromacs 4.0.2.
> > 
> > I have appended the following pull code to the mdp file:
> > 
> > ;---PULL CODE -
> > 
> > pull = umbrella
> > pull_geometry = direction
> > pull_group0 = r_500
> > pull_group1 = r_535
> > pull_vec1 = -1.306 1.355 -0.319
> > 
> > Where r_500 is the group I am expecting to be pulled,
> > r_535 - the reference (the acid that is in fact in contact with
> > r_500)
> > 
> > I have left all remaining parameters with default values. 
> > 
> > The problem is that NOTHING HAPPENED! XVG file had 0. throughout
> > simulation indicating that distance between pull group and reference
> > group was 0! 
> > 
> > 1/ What did I do wrong?
> > 2/ Is there any pull code tutorial for gromacs 4 (not previous
> > version)? 
> > 
> > Thank you!
> > SDA
> > 
> > ___
> > gmx-users mailing list gmx-users@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-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> __
> What can you do with the new Windows Live? Find out

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RE: [gmx-users] Pull Code problems


Hi,

You don't indicate which xvg file was 0, I guess pullf.xvg.
Could it be that you did not specify a force constant, meaning fc=0?

Berk

> From: gene...@gmail.com
> To: gmx-users@gromacs.org
> Date: Tue, 13 Jan 2009 14:26:47 +0300
> Subject: [gmx-users] Pull Code problems
> 
> Hello,
> 
> I am trying to run a pulling simulation with gromacs 4.0.2.
> 
> I have appended the following pull code to the mdp file:
> 
> ;---PULL CODE -
> 
> pull  =   umbrella
> pull_geometry = direction
> pull_group0   = r_500
> pull_group1   = r_535
> pull_vec1 = -1.306 1.355 -0.319
> 
> Where r_500 is the group I am expecting to be pulled,
>   r_535 - the reference (the acid that is in fact in contact with
> r_500)
> 
> I have left all remaining parameters with default values. 
> 
> The problem is that NOTHING HAPPENED! XVG file had 0. throughout
> simulation indicating that distance between pull group and reference
> group was 0! 
> 
> 1/ What did I do wrong?
> 2/ Is there any pull code tutorial for gromacs 4 (not previous
> version)? 
> 
> Thank you!
> SDA
> 
> ___
> gmx-users mailing listgmx-users@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-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

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[gmx-users] Pull Code problems