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

Wed Apr 11 21:09:36 CEST 2018

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 <jalemkul at vt.edu> 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
>>>> <nedomacho at gmail.com<mailto:nedomacho at gmail.com>> 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.greenblatt at weizmann.ac.il<mailto:harry.greenblatt at weizmann.ac.il
>>> <../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.&URL=mailto%3aharry.greenblatt%
>> 40weizmann.ac.il<http://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.greenblatt at weizmann.ac.il
>> <../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.&URL=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
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
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