Re: [gmx-users] seeming paradox with gmx wham

2018-03-12 Thread Alex 
You actually pointed this symmetry situation out when I was calculating
something that's already been submitted, so the gratitude is all mine.
Hopefully, it doesn't produce much of a difference in that particular case,
but I really should have listened. The path to correcting possible
artifacts is clear. :)

Alex

On Mon, Mar 12, 2018 at 5:03 PM, Justin Lemkul  wrote:

>
>
> On 3/12/18 6:59 PM, Alex wrote:
>
>> Great, thanks. I believe this necessitates an acknowledgment. You go by J.
>> A. Lemkul in your papers, correct?
>>
> That would work. Much obliged :)
>
> -Justin
>
>
> On Mon, Mar 12, 2018 at 4:56 PM, Justin Lemkul  wrote:
>>
>> r
>>>
>>> On 3/12/18 6:54 PM, Alex wrote:
>>>
>>> Yeah, enlarging system (4 nm to 6 nm) isn't a problem at this point, it's
 still a small system. My sampling pull code is below, I only modified
 the
 bare minimum to work with the new pull code syntax and to enable
 spherical
 slices (radius varying from near-zero to 1.5 nm):

 pull = yes
 pull-coord1-type = umbrella
 pull_ngroups= 2
 pull_ncoords= 1
 pull_group1_name= CL
 pull_group2_name= CNT
 pull_coord1_geometry= distance
 pull_coord1_groups  = 1 2
 pull_dim= Y Y Y
 pull_coord1_rate= 0.0
 pull_coord1_k   = 1000
 pull_start  = yes

 CNT is the colloquial name for our membrane. I'm trying to be
 extra-careful
 this time, so I will really appreciate if you see anything else that
 looks
 wrong. Another quick question: it is my understanding that the value of
 k
 will control the histogram width. Is 1000 a reasonable choice overall?

 No way to know. It depends on the window spacing and the forces acting
>>> in
>>> the system. I don't know that anyone has come up with a way to actually
>>> know what's "right" for umbrella sampling other than empirical
>>> assignment.
>>>
>>> Everything else looks reasonable to me.
>>>
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
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Re: [gmx-users] seeming paradox with gmx wham

2018-03-12 Thread Justin Lemkul 



On 3/12/18 6:59 PM, Alex wrote:

Great, thanks. I believe this necessitates an acknowledgment. You go by J.
A. Lemkul in your papers, correct?

That would work. Much obliged :)

-Justin


On Mon, Mar 12, 2018 at 4:56 PM, Justin Lemkul  wrote:


r

On 3/12/18 6:54 PM, Alex wrote:


Yeah, enlarging system (4 nm to 6 nm) isn't a problem at this point, it's
still a small system. My sampling pull code is below, I only modified the
bare minimum to work with the new pull code syntax and to enable spherical
slices (radius varying from near-zero to 1.5 nm):

pull = yes
pull-coord1-type = umbrella
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= CL
pull_group2_name= CNT
pull_coord1_geometry= distance
pull_coord1_groups  = 1 2
pull_dim= Y Y Y
pull_coord1_rate= 0.0
pull_coord1_k   = 1000
pull_start  = yes

CNT is the colloquial name for our membrane. I'm trying to be
extra-careful
this time, so I will really appreciate if you see anything else that looks
wrong. Another quick question: it is my understanding that the value of k
will control the histogram width. Is 1000 a reasonable choice overall?


No way to know. It depends on the window spacing and the forces acting in
the system. I don't know that anyone has come up with a way to actually
know what's "right" for umbrella sampling other than empirical assignment.

Everything else looks reasonable to me.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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==

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] seeming paradox with gmx wham

2018-03-12 Thread Alex 
Great, thanks. I believe this necessitates an acknowledgment. You go by J.
A. Lemkul in your papers, correct?

On Mon, Mar 12, 2018 at 4:56 PM, Justin Lemkul  wrote:

> r
>
> On 3/12/18 6:54 PM, Alex wrote:
>
>> Yeah, enlarging system (4 nm to 6 nm) isn't a problem at this point, it's
>> still a small system. My sampling pull code is below, I only modified the
>> bare minimum to work with the new pull code syntax and to enable spherical
>> slices (radius varying from near-zero to 1.5 nm):
>>
>> pull = yes
>> pull-coord1-type = umbrella
>> pull_ngroups= 2
>> pull_ncoords= 1
>> pull_group1_name= CL
>> pull_group2_name= CNT
>> pull_coord1_geometry= distance
>> pull_coord1_groups  = 1 2
>> pull_dim= Y Y Y
>> pull_coord1_rate= 0.0
>> pull_coord1_k   = 1000
>> pull_start  = yes
>>
>> CNT is the colloquial name for our membrane. I'm trying to be
>> extra-careful
>> this time, so I will really appreciate if you see anything else that looks
>> wrong. Another quick question: it is my understanding that the value of k
>> will control the histogram width. Is 1000 a reasonable choice overall?
>>
>
> No way to know. It depends on the window spacing and the forces acting in
> the system. I don't know that anyone has come up with a way to actually
> know what's "right" for umbrella sampling other than empirical assignment.
>
> Everything else looks reasonable to me.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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Re: [gmx-users] seeming paradox with gmx wham

2018-03-12 Thread Justin Lemkul 

r

On 3/12/18 6:54 PM, Alex wrote:

Yeah, enlarging system (4 nm to 6 nm) isn't a problem at this point, it's
still a small system. My sampling pull code is below, I only modified the
bare minimum to work with the new pull code syntax and to enable spherical
slices (radius varying from near-zero to 1.5 nm):

pull = yes
pull-coord1-type = umbrella
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= CL
pull_group2_name= CNT
pull_coord1_geometry= distance
pull_coord1_groups  = 1 2
pull_dim= Y Y Y
pull_coord1_rate= 0.0
pull_coord1_k   = 1000
pull_start  = yes

CNT is the colloquial name for our membrane. I'm trying to be extra-careful
this time, so I will really appreciate if you see anything else that looks
wrong. Another quick question: it is my understanding that the value of k
will control the histogram width. Is 1000 a reasonable choice overall?


No way to know. It depends on the window spacing and the forces acting 
in the system. I don't know that anyone has come up with a way to 
actually know what's "right" for umbrella sampling other than empirical 
assignment.


Everything else looks reasonable to me.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] seeming paradox with gmx wham

2018-03-12 Thread Alex 
Yeah, enlarging system (4 nm to 6 nm) isn't a problem at this point, it's
still a small system. My sampling pull code is below, I only modified the
bare minimum to work with the new pull code syntax and to enable spherical
slices (radius varying from near-zero to 1.5 nm):

pull = yes
pull-coord1-type = umbrella
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= CL
pull_group2_name= CNT
pull_coord1_geometry= distance
pull_coord1_groups  = 1 2
pull_dim= Y Y Y
pull_coord1_rate= 0.0
pull_coord1_k   = 1000
pull_start  = yes

CNT is the colloquial name for our membrane. I'm trying to be extra-careful
this time, so I will really appreciate if you see anything else that looks
wrong. Another quick question: it is my understanding that the value of k
will control the histogram width. Is 1000 a reasonable choice overall?

Thank you,

Alex

On Mon, Mar 12, 2018 at 4:07 PM, Justin Lemkul  wrote:

>
>
> On 3/12/18 3:42 PM, Alex wrote:
>
>> I actually understood your tutorial perfectly well. What I didn't expect
>> is such a significant dependence on direction (assuming spherical symmetry
>> clears the situation).
>>
>> I also had to use direction-periodic instead of distance in your
>> tutorial, because the box is 4 nm wide and grompp is screaming about
>> distance exceeding half-box size. I used 5.0.3 before and it was fine with
>> the 'distance' directive. I think 'direction-periodic' is also wrong for
>> spherical symmetry. So, stick with distance and increase box size?
>>
>> That's the easiest thing to do, yes, as long as the simulation is still
> reasonably efficient.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] seeming paradox with gmx wham

2018-03-12 Thread Justin Lemkul 



On 3/12/18 3:42 PM, Alex wrote:
I actually understood your tutorial perfectly well. What I didn't 
expect is such a significant dependence on direction (assuming 
spherical symmetry clears the situation).


I also had to use direction-periodic instead of distance in your 
tutorial, because the box is 4 nm wide and grompp is screaming about 
distance exceeding half-box size. I used 5.0.3 before and it was fine 
with the 'distance' directive. I think 'direction-periodic' is also 
wrong for spherical symmetry. So, stick with distance and increase box 
size?


That's the easiest thing to do, yes, as long as the simulation is still 
reasonably efficient.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] seeming paradox with gmx wham

2018-03-12 Thread Alex 

Sorry, i meant 4 nm tall, not wide.


On 3/12/2018 1:42 PM, Alex wrote:
I actually understood your tutorial perfectly well. What I didn't 
expect is such a significant dependence on direction (assuming 
spherical symmetry clears the situation).


I also had to use direction-periodic instead of distance in your 
tutorial, because the box is 4 nm wide and grompp is screaming about 
distance exceeding half-box size. I used 5.0.3 before and it was fine 
with the 'distance' directive. I think 'direction-periodic' is also 
wrong for spherical symmetry. So, stick with distance and increase box 
size?


Thanks,

Alex


On 3/12/2018 1:35 PM, Justin Lemkul wrote:



On 3/12/18 3:28 PM, Alex wrote:

Thanks!

Just to make sure I'm doing this right this time. By merely changing 
the dim directive with everything else following your tutorial, I 
would be probing the spherical domain around the pore with a bunch 
of different radius values? Because this is exactly what I want.




Yes, you're applying a 1-D bias when you actually want a 3-D bias. 
People often misuse the tutorial .mdp files, though I will have a new 
version of the tutorial out this summer (along with a paper) that 
should clear all this up.


-Justin


Thanks,

Alex


On 3/12/2018 8:43 AM, Justin Lemkul wrote:



On 3/11/18 8:05 PM, Alex wrote:
Just to add to my question... The pull code for the umbrella 
sampling from each of the N configs, as used in Justin's tutorial, is


pull_coord1_type    = umbrella
pull_coord1_geometry    = distance
...
pull_coord1_dim = N N Y

So, in each of the generated pullf and pullx files we sample a 
flat slice at a given Z, and the reported forces and displacements 
are along Z. What appears to be the reaction coordinate in our 
case is the radius from the pore mouth, and one has to sample a 
set of hemispheres from a series of radius values. Is this at all 
a possibility?




Yes, but not by following the tutorial. You'd need to use 
pull_coord1_dim = Y Y Y to restrict the ions to a given radius 
around the pore itself. As it is, you're probably underestimating 
entropic contributions to the free energy.


-Justin









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Re: [gmx-users] seeming paradox with gmx wham

2018-03-12 Thread Alex 
I actually understood your tutorial perfectly well. What I didn't expect 
is such a significant dependence on direction (assuming spherical 
symmetry clears the situation).


I also had to use direction-periodic instead of distance in your 
tutorial, because the box is 4 nm wide and grompp is screaming about 
distance exceeding half-box size. I used 5.0.3 before and it was fine 
with the 'distance' directive. I think 'direction-periodic' is also 
wrong for spherical symmetry. So, stick with distance and increase box size?


Thanks,

Alex


On 3/12/2018 1:35 PM, Justin Lemkul wrote:



On 3/12/18 3:28 PM, Alex wrote:

Thanks!

Just to make sure I'm doing this right this time. By merely changing 
the dim directive with everything else following your tutorial, I 
would be probing the spherical domain around the pore with a bunch of 
different radius values? Because this is exactly what I want.




Yes, you're applying a 1-D bias when you actually want a 3-D bias. 
People often misuse the tutorial .mdp files, though I will have a new 
version of the tutorial out this summer (along with a paper) that 
should clear all this up.


-Justin


Thanks,

Alex


On 3/12/2018 8:43 AM, Justin Lemkul wrote:



On 3/11/18 8:05 PM, Alex wrote:
Just to add to my question... The pull code for the umbrella 
sampling from each of the N configs, as used in Justin's tutorial, is


pull_coord1_type    = umbrella
pull_coord1_geometry    = distance
...
pull_coord1_dim = N N Y

So, in each of the generated pullf and pullx files we sample a flat 
slice at a given Z, and the reported forces and displacements are 
along Z. What appears to be the reaction coordinate in our case is 
the radius from the pore mouth, and one has to sample a set of 
hemispheres from a series of radius values. Is this at all a 
possibility?




Yes, but not by following the tutorial. You'd need to use 
pull_coord1_dim = Y Y Y to restrict the ions to a given radius 
around the pore itself. As it is, you're probably underestimating 
entropic contributions to the free energy.


-Justin







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Re: [gmx-users] seeming paradox with gmx wham

2018-03-12 Thread Justin Lemkul 



On 3/12/18 3:28 PM, Alex wrote:

Thanks!

Just to make sure I'm doing this right this time. By merely changing 
the dim directive with everything else following your tutorial, I 
would be probing the spherical domain around the pore with a bunch of 
different radius values? Because this is exactly what I want.




Yes, you're applying a 1-D bias when you actually want a 3-D bias. 
People often misuse the tutorial .mdp files, though I will have a new 
version of the tutorial out this summer (along with a paper) that should 
clear all this up.


-Justin


Thanks,

Alex


On 3/12/2018 8:43 AM, Justin Lemkul wrote:



On 3/11/18 8:05 PM, Alex wrote:
Just to add to my question... The pull code for the umbrella 
sampling from each of the N configs, as used in Justin's tutorial, is


pull_coord1_type    = umbrella
pull_coord1_geometry    = distance
...
pull_coord1_dim = N N Y

So, in each of the generated pullf and pullx files we sample a flat 
slice at a given Z, and the reported forces and displacements are 
along Z. What appears to be the reaction coordinate in our case is 
the radius from the pore mouth, and one has to sample a set of 
hemispheres from a series of radius values. Is this at all a 
possibility?




Yes, but not by following the tutorial. You'd need to use 
pull_coord1_dim = Y Y Y to restrict the ions to a given radius around 
the pore itself. As it is, you're probably underestimating entropic 
contributions to the free energy.


-Justin





--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] seeming paradox with gmx wham

2018-03-12 Thread Alex 

Thanks!

Just to make sure I'm doing this right this time. By merely changing the 
dim directive with everything else following your tutorial, I would be 
probing the spherical domain around the pore with a bunch of different 
radius values? Because this is exactly what I want.


Thanks,

Alex


On 3/12/2018 8:43 AM, Justin Lemkul wrote:



On 3/11/18 8:05 PM, Alex wrote:
Just to add to my question... The pull code for the umbrella sampling 
from each of the N configs, as used in Justin's tutorial, is


pull_coord1_type    = umbrella
pull_coord1_geometry    = distance
...
pull_coord1_dim = N N Y

So, in each of the generated pullf and pullx files we sample a flat 
slice at a given Z, and the reported forces and displacements are 
along Z. What appears to be the reaction coordinate in our case is 
the radius from the pore mouth, and one has to sample a set of 
hemispheres from a series of radius values. Is this at all a 
possibility?




Yes, but not by following the tutorial. You'd need to use 
pull_coord1_dim = Y Y Y to restrict the ions to a given radius around 
the pore itself. As it is, you're probably underestimating entropic 
contributions to the free energy.


-Justin



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Re: [gmx-users] seeming paradox with gmx wham

2018-03-12 Thread Justin Lemkul 



On 3/11/18 8:05 PM, Alex wrote:
Just to add to my question... The pull code for the umbrella sampling 
from each of the N configs, as used in Justin's tutorial, is


pull_coord1_type    = umbrella
pull_coord1_geometry    = distance
...
pull_coord1_dim = N N Y

So, in each of the generated pullf and pullx files we sample a flat 
slice at a given Z, and the reported forces and displacements are 
along Z. What appears to be the reaction coordinate in our case is the 
radius from the pore mouth, and one has to sample a set of hemispheres 
from a series of radius values. Is this at all a possibility?




Yes, but not by following the tutorial. You'd need to use 
pull_coord1_dim = Y Y Y to restrict the ions to a given radius around 
the pore itself. As it is, you're probably underestimating entropic 
contributions to the free energy.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] seeming paradox with gmx wham

2018-03-11 Thread Alex 

Just to add to my question... The pull code for the umbrella sampling from each 
of the N configs, as used in Justin's tutorial, is

pull_coord1_type= umbrella
pull_coord1_geometry= distance
...
pull_coord1_dim = N N Y

So, in each of the generated pullf and pullx files we sample a flat slice at a 
given Z, and the reported forces and displacements are along Z. What appears to 
be the reaction coordinate in our case is the radius from the pore mouth, and 
one has to sample a set of hemispheres from a series of radius values. Is this 
at all a possibility?

Alex


On 3/11/2018 5:37 PM, Alex wrote:

Hi all,

I am looking at what appears to be a paradox. Consider the following 
situation: we have a graphene membrane with a single pore of a 
particular type. The pore is located at (x0, y0, h/2), where h is the 
box height. The membrane is position-restrained along its perimeter 
and immersed in a solution of NaCl. The pore is designed to trap 
anions -- and it does, if you artificially bring an anion close enough 
to the mouth of the pore and run the simulation at, say, room temp.


However, the ions do not bind by themselves. 100s of nanoseconds of 
simulations with high salt concentrations -- nothing. So, I expect a 
high barrier associated with ion dehydration when entering the pore. 
Following Justin's tutorial and generating a total of 30 1A-spaced 
configs (15 below h/2, 15 above h/2) along (x0,y0), gmx wham yields a 
6.5 kJ/mol barrier, which isn't high at all! Just from the pullf data 
when generating the configs (pull along Z with x and y restrained), 
the naive integral of the pulling force prior to overcoming the 
hydration barrier yields 4 kJ/mol -- consistent with the WHAM result. 
But in reality, ions (which aren't restrained around (x0,y0) are not 
observed to bind, which brings us to my question...


It looks like when an ion approaches the pore parallel to the membrane 
normal, the barrier is indeed low, while approach at an angle yields 
higher barriers. It appears that WHAM produces the free energy curve 
resulting from frequent sampling approach directions that have the 
lowest possible barrier. Is it possible to modify this calculation to 
give equal weight to all approach directions?


Thank you,

Alex




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