[gmx-users] couple-intramol

[Justin Lemkul]

On 1/4/17 10:25 AM, qasimpars at gmail.com wrote:
> Hi,
>
> What should I select from the edr file to get the intramolecular energy of the ligand after mdrun -rerun?  Only Coul-SR and LJ-SR?
>

No, as again that would just be some of the nonbonded components.

If you run a simulation of just a ligand, and calculate its energy, the energy 
of the system = the energy of the ligand.

-Justin

> Thanks.
>
>
>
>> On 4 Jan 2017, at 16:08, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>
>>> On 1/4/17 12:10 AM, Qasim Pars wrote:
>>> Hi,
>>>
>>> Thanks. If I want to calculate the intramolecular energy of the ligand, I
>>> need to choose Coul-14:LIG-LIG, LJ-14:LIG-LIG, Coul-SR:LIG-LIG and
>>> LJ-SR:LIG-LIG in the .edr file. Am I wrong?
>>
>> Those would be the nonbonded components of the ligand's energy but it is not the intramolecular energy of the ligand.  That would include bonded terms, which are not decomposed via energygrps.  You'd have to extract the ligand coordinates from the trajectory, make a matching .tpr file (via gmx convert-tpr) and use mdrun -rerun to calculate the total intramolecular energy.
>>
>> -Justin
>>
>>>> On 4 January 2017 at 04:03, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>>
>>>>> On 1/3/17 2:40 PM, Qasim Pars wrote:
>>>>>
>>>>> Dear users,
>>>>>
>>>>> I got a little bit confused about the use of "couple-intramol". If I set
>>>>> it
>>>>> to "no", the intramolecular intractions of the ligand are "on" when the
>>>>> ligand is decoupled, right? It means that I don't need to set [
>>>>
>>>> More specifically, intramolecular interactions are not a function of
>>>> lambda; they are always in the A-state.  Only intermolecular interactions
>>>> are modulated by lambda.
>>>>
>>>> nonbond_params ] part for the ligand?
>>>> You should never have to do anything with [nonbond_params] in these
>>>> systems.
>>>>
>>>> -Justin
>>>>
>>>> ; Free energy
>>>>> free-energy              = yes
>>>>> init-lambda              = 0
>>>>> delta-lambda             = 0
>>>>> sc-alpha                 = 0.5
>>>>> sc-power                 = 1
>>>>> sc-sigma                 = 0.3
>>>>> sc-coul                  = yes
>>>>> couple-moltype           = ligand
>>>>> couple-intramol          = no
>>>>> couple-lambda0           = vdw-q
>>>>> couple-lambda1           = none
>>>>> nstdhdl                  = 100
>>>>>
>>>>> Thanks in advance,
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>
>>>> Department of Pharmaceutical Sciences
>>>> School of Pharmacy
>>>> Health Sciences Facility II, Room 629
>>>> University of Maryland, Baltimore
>>>> 20 Penn St.
>>>> Baltimore, MD 21201
>>>>
>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>
>>>> ==================================================
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>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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>> Gromacs Users mailing list
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>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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