Re: [gmx-users] affect of water removal on subsequent energy calculations

2018-04-11 Thread Alex
For an additive force field, the two numbers are in agreement, E_tot - 
E_13 - E_23 - E_33 = E_12, by definition. You can easily design a test 
case that will prove this.



I know. I have it in front of me. ;)
The dielectric constant of the medium is not included in the 
calculation, at least not explicitly, but its effects are there in the 
calculation of the forces. GROMACS lets you mess with the relative 
dielectric via epsilon_r in the .mdp file, but if you do that, you 
break the force field. All modern force fields and the water models 
that go along with them assume they are being parametrized relative to 
vacuum permittivity, as explained by Erik in e.g.:
And that is precisely what I said in my initial post here. However, I 
suppose I was incorrect when saying that water trajectories would make a 
difference for what the original topicstarter was asking about energies. 
There is a difference for what we're trying to do, though, as we do want 
to see distributions and not energies calculated with an approximate 
value of epsilon. That whole concept of dielectric constant breaks down 
for high confinement.


Alex

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Re: [gmx-users] affect of water removal on subsequent energy calculations

2018-04-11 Thread Justin Lemkul



On 4/11/18 3:09 PM, Alex wrote:

Mark, Justin:

This is two against one, even though noone was questioning the 
additivity of energy in forcefields with constant charges, etc.


So, let's go back specifically to solvation. Consider a system with 
two oppositely charged ions (1 and 2) in water of your choosing (group 
3). For extreme simplicity, the ions are actually restrained at a 
distance R from each other, and again for simplicity we're only 
interested in the Coulomb part of the potential energy. The trajectory 
contains everything.


In one instance, we calculate E_tot - E_13 - E_23 - E_33, in another 
E_12 (as one would easily do for a trajectory that has no water 
coordinates). Are those two numbers in agreement and, if so, what is 
it? q1*q2/R or q1*q2/eps/R?




For an additive force field, the two numbers are in agreement, E_tot - 
E_13 - E_23 - E_33 = E_12, by definition. You can easily design a test 
case that will prove this.


The dielectric constant of the medium is not included in the 
calculation, at least not explicitly, but its effects are there in the 
calculation of the forces. GROMACS lets you mess with the relative 
dielectric via epsilon_r in the .mdp file, but if you do that, you break 
the force field. All modern force fields and the water models that go 
along with them assume they are being parametrized relative to vacuum 
permittivity, as explained by Erik in e.g.:


https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2004-March/009650.html 



As a result of this convention, water models are parametrized to 
approximate the dielectric constant of water based on their charge 
distribution and hence the forces competing for interactions among 
charged particles to model the screening effect. This is different from 
an implicit or MM/PBSA-type calculation, of course, where setting a 
solvent dielectric is necessary and part of the calculation to compute 
terms in the energy function. In an additive MM force field, the effect 
is baked into the parametrization of the model.


-Justin

--

==

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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.thelemkullab.com

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Re: [gmx-users] affect of water removal on subsequent energy calculations

2018-04-11 Thread Alex

Mark, Justin:

This is two against one, even though noone was questioning the 
additivity of energy in forcefields with constant charges, etc.


So, let's go back specifically to solvation. Consider a system with two 
oppositely charged ions (1 and 2) in water of your choosing (group 3). 
For extreme simplicity, the ions are actually restrained at a distance R 
from each other, and again for simplicity we're only interested in the 
Coulomb part of the potential energy. The trajectory contains everything.


In one instance, we calculate E_tot - E_13 - E_23 - E_33, in another 
E_12 (as one would easily do for a trajectory that has no water 
coordinates). Are those two numbers in agreement and, if so, what is it? 
q1*q2/R or q1*q2/eps/R?


Alex


On 4/11/2018 5:37 AM, Mark Abraham wrote:

Hi,

What Justin said, plus the observation that you should know how you plan to
analyze the results before you run the simulation. In this case, that means
knowing what you'll learn from rerun energies. Sometimes this means that
you won't ever run the simulations, and those are the really efficient ones
;-)

Mark

On Wed, Apr 11, 2018 at 1:29 PM Justin Lemkul  wrote:



On 4/11/18 4:21 AM, Alex wrote:

Screening effects in Gromacs come in a rather non-straightforward
manner in terms of data extraction: they certainly exist within the
simulations in the form of the fields induced by local water
orientation, but to extract them from reruns is extremely challenging
even if you're outputting water trajectories. If this is about
interactions between different parts of proteins, I would absolutely
output water trajectories, because otherwise you're left with
LJ+electrostatics and assumptions on local dielectric constant, which
in itself is a very nuanced problem:
https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.99.077801


The reality isn't this complex for fixed-charge, additive force fields.
The fundamental truth of a pairwise additive potential is that in a
mixture of A+B+C, then the interaction energy of A-B in a given
configuration does not depend in any way on C. So if C=water, then you
should get the exact same interaction energy from a fully solvated or a
fully desolvated system. This is not true when multibody terms are
involved (polarizable force fields or actual, physical reality) but for
the simple purpose of computing interaction energies, the waters are
irrelevant.

That said, unless the force field has been parametrized in a way that
makes interaction energies physical valid or useful, the quantity itself
means very little.

-Justin


We're faced with very similar challenges at the moment, so we're
independently postprocessing complete trajectories (including
everything) and solving Poisson's eqn all over again to give e.g.
time-averaged 3D electrostatics maps.

Alex


On 4/11/2018 1:56 AM, Harry Mark Greenblatt wrote:

BS”D

   Dear Alex,

Not *explicitly* related to water:  we would like to look at
interaction energies between parts of proteins, or proteins and DNA.
So screening comes to mind…


Harry


On 11 Apr 2018, at 10:51 AM, Alex
> wrote:

If you plan to extract anything explicitly related to water from your
reruns -- very much so. Basically unusable trajectories.

Alex


On 4/11/2018 1:48 AM, Harry Mark Greenblatt wrote:
B”SD

In an effort to reduce the size of output xtc files of simulations of
large systems, we thought of saving these files without water molecules.

It occurred to us, however, that upon subsequent cpu-only reruns
in order to do energy calculations, these results would be adversely
affected, since the water molecules are not stored in the xtc file.

Is this indeed a concern?

Thanks

Harry




Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology
harry.greenbl...@weizmann.ac.il>

Weizmann Institute of SciencePhone:  972-8-934-6340
234 Herzl St.Facsimile:   972-8-934-3361
Rehovot, 7610001
Israel


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Associate Staff Scientist
Dept of Structural Biology
harry.greenbl...@weizmann.ac.il

<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.=mailto%3aharry.greenblatt%

Re: [gmx-users] affect of water removal on subsequent energy calculations

2018-04-11 Thread Mark Abraham
Hi,

What Justin said, plus the observation that you should know how you plan to
analyze the results before you run the simulation. In this case, that means
knowing what you'll learn from rerun energies. Sometimes this means that
you won't ever run the simulations, and those are the really efficient ones
;-)

Mark

On Wed, Apr 11, 2018 at 1:29 PM Justin Lemkul  wrote:

>
>
> On 4/11/18 4:21 AM, Alex wrote:
> > Screening effects in Gromacs come in a rather non-straightforward
> > manner in terms of data extraction: they certainly exist within the
> > simulations in the form of the fields induced by local water
> > orientation, but to extract them from reruns is extremely challenging
> > even if you're outputting water trajectories. If this is about
> > interactions between different parts of proteins, I would absolutely
> > output water trajectories, because otherwise you're left with
> > LJ+electrostatics and assumptions on local dielectric constant, which
> > in itself is a very nuanced problem:
> > https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.99.077801
> >
>
> The reality isn't this complex for fixed-charge, additive force fields.
> The fundamental truth of a pairwise additive potential is that in a
> mixture of A+B+C, then the interaction energy of A-B in a given
> configuration does not depend in any way on C. So if C=water, then you
> should get the exact same interaction energy from a fully solvated or a
> fully desolvated system. This is not true when multibody terms are
> involved (polarizable force fields or actual, physical reality) but for
> the simple purpose of computing interaction energies, the waters are
> irrelevant.
>
> That said, unless the force field has been parametrized in a way that
> makes interaction energies physical valid or useful, the quantity itself
> means very little.
>
> -Justin
>
> > We're faced with very similar challenges at the moment, so we're
> > independently postprocessing complete trajectories (including
> > everything) and solving Poisson's eqn all over again to give e.g.
> > time-averaged 3D electrostatics maps.
> >
> > Alex
> >
> >
> > On 4/11/2018 1:56 AM, Harry Mark Greenblatt wrote:
> >> BS”D
> >>
> >>   Dear Alex,
> >>
> >>Not *explicitly* related to water:  we would like to look at
> >> interaction energies between parts of proteins, or proteins and DNA.
> >> So screening comes to mind…
> >>
> >>
> >> Harry
> >>
> >>
> >> On 11 Apr 2018, at 10:51 AM, Alex
> >> > wrote:
> >>
> >> If you plan to extract anything explicitly related to water from your
> >> reruns -- very much so. Basically unusable trajectories.
> >>
> >> Alex
> >>
> >>
> >> On 4/11/2018 1:48 AM, Harry Mark Greenblatt wrote:
> >> B”SD
> >>
> >> In an effort to reduce the size of output xtc files of simulations of
> >> large systems, we thought of saving these files without water molecules.
> >>
> >>It occurred to us, however, that upon subsequent cpu-only reruns
> >> in order to do energy calculations, these results would be adversely
> >> affected, since the water molecules are not stored in the xtc file.
> >>
> >> Is this indeed a concern?
> >>
> >> Thanks
> >>
> >> Harry
> >>
> >>
> >>
> >> 
> >> Harry M. Greenblatt
> >> Associate Staff Scientist
> >> Dept of Structural Biology
> >> harry.greenbl...@weizmann.ac.il ><../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.=mailto%3aharry.greenblatt%
> 40weizmann.ac.il>
> >> Weizmann Institute of SciencePhone:  972-8-934-6340
> >> 234 Herzl St.Facsimile:   972-8-934-3361
> >> Rehovot, 7610001
> >> Israel
> >>
> >>
> >> --
> >> 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.
> >>
> >>
> >> 
> >> Harry M. Greenblatt
> >> Associate Staff Scientist
> >> Dept of Structural Biology
> >> harry.greenbl...@weizmann.ac.il
> <../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.=mailto%3aharry.greenblatt%
> 40weizmann.ac.il>
> >> Weizmann Institute of SciencePhone:  972-8-934-6340
> >> 234 Herzl St.Facsimile:   972-8-934-3361
> >> Rehovot, 7610001
> >> Israel
> >>
> >
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel 

Re: [gmx-users] affect of water removal on subsequent energy calculations

2018-04-11 Thread Justin Lemkul



On 4/11/18 4:21 AM, Alex wrote:
Screening effects in Gromacs come in a rather non-straightforward 
manner in terms of data extraction: they certainly exist within the 
simulations in the form of the fields induced by local water 
orientation, but to extract them from reruns is extremely challenging 
even if you're outputting water trajectories. If this is about 
interactions between different parts of proteins, I would absolutely 
output water trajectories, because otherwise you're left with 
LJ+electrostatics and assumptions on local dielectric constant, which 
in itself is a very nuanced problem: 
https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.99.077801




The reality isn't this complex for fixed-charge, additive force fields. 
The fundamental truth of a pairwise additive potential is that in a 
mixture of A+B+C, then the interaction energy of A-B in a given 
configuration does not depend in any way on C. So if C=water, then you 
should get the exact same interaction energy from a fully solvated or a 
fully desolvated system. This is not true when multibody terms are 
involved (polarizable force fields or actual, physical reality) but for 
the simple purpose of computing interaction energies, the waters are 
irrelevant.


That said, unless the force field has been parametrized in a way that 
makes interaction energies physical valid or useful, the quantity itself 
means very little.


-Justin

We're faced with very similar challenges at the moment, so we're 
independently postprocessing complete trajectories (including 
everything) and solving Poisson's eqn all over again to give e.g. 
time-averaged 3D electrostatics maps.


Alex


On 4/11/2018 1:56 AM, Harry Mark Greenblatt wrote:

BS”D

  Dear Alex,

   Not *explicitly* related to water:  we would like to look at 
interaction energies between parts of proteins, or proteins and DNA.  
So screening comes to mind…



Harry


On 11 Apr 2018, at 10:51 AM, Alex 
> wrote:


If you plan to extract anything explicitly related to water from your 
reruns -- very much so. Basically unusable trajectories.


Alex


On 4/11/2018 1:48 AM, Harry Mark Greenblatt wrote:
B”SD

In an effort to reduce the size of output xtc files of simulations of 
large systems, we thought of saving these files without water molecules.


   It occurred to us, however, that upon subsequent cpu-only reruns 
in order to do energy calculations, these results would be adversely 
affected, since the water molecules are not stored in the xtc file.


Is this indeed a concern?

Thanks

Harry




Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology 
harry.greenbl...@weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.=mailto%3aharry.greenblatt%40weizmann.ac.il>

Weizmann Institute of Science    Phone:  972-8-934-6340
234 Herzl St.    Facsimile:   972-8-934-3361
Rehovot, 7610001
Israel


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Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology 
harry.greenbl...@weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.=mailto%3aharry.greenblatt%40weizmann.ac.il>

Weizmann Institute of Science    Phone:  972-8-934-6340
234 Herzl St.    Facsimile:   972-8-934-3361
Rehovot, 7610001
Israel





--
==

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.thelemkullab.com

==

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Re: [gmx-users] affect of water removal on subsequent energy calculations

2018-04-11 Thread Harry Mark Greenblatt
BS”D

Ok, thanks for the advice,


Harry


On 11 Apr 2018, at 11:21 AM, Alex 
> wrote:

Screening effects in Gromacs come in a rather non-straightforward manner in 
terms of data extraction: they certainly exist within the simulations in the 
form of the fields induced by local water orientation, but to extract them from 
reruns is extremely challenging even if you're outputting water trajectories. 
If this is about interactions between different parts of proteins, I would 
absolutely output water trajectories, because otherwise you're left with 
LJ+electrostatics and assumptions on local dielectric constant, which in itself 
is a very nuanced problem: 
https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.99.077801

We're faced with very similar challenges at the moment, so we're independently 
postprocessing complete trajectories (including everything) and solving 
Poisson's eqn all over again to give e.g. time-averaged 3D electrostatics maps.




Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology   
harry.greenbl...@weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.=mailto%3aharry.greenblatt%40weizmann.ac.il>
Weizmann Institute of SciencePhone:  972-8-934-6340
234 Herzl St.Facsimile:   972-8-934-3361
Rehovot, 7610001
Israel

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Re: [gmx-users] affect of water removal on subsequent energy calculations

2018-04-11 Thread Alex
Screening effects in Gromacs come in a rather non-straightforward manner 
in terms of data extraction: they certainly exist within the simulations 
in the form of the fields induced by local water orientation, but to 
extract them from reruns is extremely challenging even if you're 
outputting water trajectories. If this is about interactions between 
different parts of proteins, I would absolutely output water 
trajectories, because otherwise you're left with LJ+electrostatics and 
assumptions on local dielectric constant, which in itself is a very 
nuanced problem: 
https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.99.077801


We're faced with very similar challenges at the moment, so we're 
independently postprocessing complete trajectories (including 
everything) and solving Poisson's eqn all over again to give e.g. 
time-averaged 3D electrostatics maps.


Alex


On 4/11/2018 1:56 AM, Harry Mark Greenblatt wrote:

BS”D

  Dear Alex,

   Not *explicitly* related to water:  we would like to look at interaction 
energies between parts of proteins, or proteins and DNA.  So screening comes to 
mind…


Harry


On 11 Apr 2018, at 10:51 AM, Alex 
> wrote:

If you plan to extract anything explicitly related to water from your reruns -- 
very much so. Basically unusable trajectories.

Alex


On 4/11/2018 1:48 AM, Harry Mark Greenblatt wrote:
B”SD

In an effort to reduce the size of output xtc files of simulations of large 
systems, we thought of saving these files without water molecules.

   It occurred to us, however, that upon subsequent cpu-only reruns in order to 
do energy calculations, these results would be adversely affected, since the 
water molecules are not stored in the xtc file.

Is this indeed a concern?

Thanks

Harry




Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology   
harry.greenbl...@weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.=mailto%3aharry.greenblatt%40weizmann.ac.il>
Weizmann Institute of SciencePhone:  972-8-934-6340
234 Herzl St.Facsimile:   972-8-934-3361
Rehovot, 7610001
Israel


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Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology   
harry.greenbl...@weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.=mailto%3aharry.greenblatt%40weizmann.ac.il>
Weizmann Institute of SciencePhone:  972-8-934-6340
234 Herzl St.Facsimile:   972-8-934-3361
Rehovot, 7610001
Israel



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Re: [gmx-users] affect of water removal on subsequent energy calculations

2018-04-11 Thread Harry Mark Greenblatt
BS”D

 Dear Alex,

  Not *explicitly* related to water:  we would like to look at interaction 
energies between parts of proteins, or proteins and DNA.  So screening comes to 
mind…


Harry


On 11 Apr 2018, at 10:51 AM, Alex 
> wrote:

If you plan to extract anything explicitly related to water from your reruns -- 
very much so. Basically unusable trajectories.

Alex


On 4/11/2018 1:48 AM, Harry Mark Greenblatt wrote:
B”SD

In an effort to reduce the size of output xtc files of simulations of large 
systems, we thought of saving these files without water molecules.

  It occurred to us, however, that upon subsequent cpu-only reruns in order to 
do energy calculations, these results would be adversely affected, since the 
water molecules are not stored in the xtc file.

Is this indeed a concern?

Thanks

Harry




Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology   
harry.greenbl...@weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.=mailto%3aharry.greenblatt%40weizmann.ac.il>
Weizmann Institute of SciencePhone:  972-8-934-6340
234 Herzl St.Facsimile:   972-8-934-3361
Rehovot, 7610001
Israel


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Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology   
harry.greenbl...@weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.=mailto%3aharry.greenblatt%40weizmann.ac.il>
Weizmann Institute of SciencePhone:  972-8-934-6340
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Re: [gmx-users] affect of water removal on subsequent energy calculations

2018-04-11 Thread Alex
If you plan to extract anything explicitly related to water from your 
reruns -- very much so. Basically unusable trajectories.


Alex


On 4/11/2018 1:48 AM, Harry Mark Greenblatt wrote:

B”SD

In an effort to reduce the size of output xtc files of simulations of large 
systems, we thought of saving these files without water molecules.

   It occurred to us, however, that upon subsequent cpu-only reruns in order to 
do energy calculations, these results would be adversely affected, since the 
water molecules are not stored in the xtc file.

Is this indeed a concern?

Thanks

Harry




Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology   
harry.greenbl...@weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.=mailto%3aharry.greenblatt%40weizmann.ac.il>
Weizmann Institute of SciencePhone:  972-8-934-6340
234 Herzl St.Facsimile:   972-8-934-3361
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Israel



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