[gmx-users] Interaction energy

[Justin Lemkul]

On 1/5/19 4:09 AM, rose rahmani wrote:
> How can i find these information about charmm forcefield? Would you please
> help me?

There are many review articles available about its parametrization 
methodology and development history. Start there.

The key is that CHARMM charges and LJ parameters are explicitly tuned 
against QM water interaction energies. So the force field is 
intrinsically balanced against a "real" standard (real assuming the QM 
method is sufficiently accurate).

-Justin

> On Tue, 27 Nov 2018, 00:22 Mark Abraham <mark.j.abraham at gmail.com wrote:
>
>> Hi,
>>
>> On Mon, Nov 26, 2018 at 7:47 PM Nick Johans <johans.nick93 at gmail.com>
>> wrote:
>>
>>> On Mon, 26 Nov 2018, 21:28 Justin Lemkul <jalemkul at vt.edu wrote:
>>>
>>>>
>>>> On 11/26/18 10:51 AM, Nick Johans wrote:
>>>>> On Mon, 26 Nov 2018, 18:22 Justin Lemkul <jalemkul at vt.edu wrote:
>>>>>
>>>>>> On 11/22/18 11:41 AM, Nick Johans wrote:
>>>>>>> Hi
>>>>>>>
>>>>>>> I am beginner in MD. Maybe it is not a wise question but i want to
>>>>>>> calculate the interaction energy between protein and ligand and
>> also
>>>> PMF
>>>>>> in
>>>>>>> different distances. But i don't know what is the didference
>> between
>>>>>> PMF, i
>>>>>>> mean free energy in particular(by umbrella sampling) and the
>>>> interaction
>>>>>>> energy (by g_energy tool) in my case?
>>>>>> Interaction energy is a pairwise decomposition of short-range
>>> nonbonded
>>>>>> interaction energy in the system. This energy is usually not
>>> physically
>>>>>> meaningful, but if the force field has been parametrized in such a
>> way
>>>>>> that it is, the interaction energy is a contribution to the enthalpy
>>> of
>>>>>> the system.
>>>>>>
>>>>> What forcefields embedded in GROMACS do, yes?
>>>> AFAIK only CHARMM.
>>>>
>>> Interesting! You mean interaction energy calculated by for example AMBER
>>> may not be true? Why?? What makes CHARMM unique??
>>>
>> As Justin said, the difference is in the way it is parametrized.
>> Forcefields are generally built to be additive, but it does not follow that
>> they are decomposable.
>>
>>>> If coulomb energy is also existed between pairs, so the interaction
>>>> energy
>>>>> will be LJ+Coulomb yes?
>>>> Pairs are 1-4 (intramolecular) interactions, so if you define
>>>> interaction energy between two nonbonded species, you'll get zeroes for
>>>> all the pair energies, by definition.
>>>>
>>> It's exactly the SR(short range) selection in g_energy, yes?
>>
>> You seem to be using a looser definition of pairs than is usual in
>> discussion of GROMACS topologies.
>>
>>
>>> all long range
>>> are zero.
>>
>> If there's a long-range model, then such interactions are not uniformly of
>> zero magnitude...
>>
>>
>>> But coulomb and LJ are non-zero. So, in this case the interaction
>>> energy would be
>>> Short range LJ+ Short range Coulomb , true?
>>>
>> As far as I'm concerned, you can invent whatever quantity you want, but the
>> burden is on you to demonstrate that there's a reason to connect it to
>> something physical.
>>
>> Mark
>>
>>
>>>>> So what about PMF. It seems like an interaction energy too, but more
>>>>> accurate one???
>>>> That's not what a PMF is. A PMF is the change in free energy of a
>> system
>>>> as a function of progress along a reaction coordinate.
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Assistant Professor
>>>> Office: 301 Fralin Hall
>>>> Lab: 303 Engel Hall
>>>>
>>>> Virginia Tech Department of Biochemistry
>>>> 340 West Campus Dr.
>>>> Blacksburg, VA 24061
>>>>
>>>> jalemkul at vt.edu | (540) 231-3129
>>>> http://www.thelemkullab.com
>>>>
>>>> ==================================================
>>>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================