[gmx-users] Dihedral drivers and 2D Energy Plot in gromacs
Devashish_Das
dasdevashishdas at gmail.com
Wed Mar 22 00:02:11 CET 2017
Thanks for the solution.
So, Is it not possible to do 2D-energy plot of AIB-dipeptide with a water
box? or only the use of constant box is the problem?
On Mon, Mar 20, 2017 at 5:26 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 3/20/17 2:50 AM, Devashish_Das wrote:
>
>> Thanks for the reply.
>> The problem now I am facing is, the total energy ( 15960125.0 kJ/mol for
>> 180-180
>> degree) and dihderal restraint (Its coming like 0.594114 for 180-180
>> degree).
>> What I am currently trying is:
>>
>> 1. Take the AIB dipeptide and do minimization in vacuum to get the nearly
>> angle
>> of Phi-Psi desired (I am doing it for every 10 degree)
>> 2. Add water box manually to the minimized AIB.gro file (For keeping the
>> number
>> of water molecule exactly same?)
>> 3. Minimize the system again with restraints.
>> 4. remove the restraints from the .top file and use a normal .mdp file for
>> generating .tpr file
>> 5. Use this tpr and minimized gro file with water to do mdrun -rerun
>> 6. Use gmx energy to calculate "Total Energy" from the rerun.edr and
>> "Dihedral
>> Restraint" from AIB_water_minimized.edr file
>> 7. Plot the final Energy (= (Total Energy - Dihedral Restraint Energy) -
>> minimum
>> of the list)
>>
>> Am I doing this right?
>>
>>
> No, you shouldn't be involving water at all, and the manual overlay of the
> same water box on every system is undoubtedly going to cause atomic overlap
> that leads to the bizarre energies.
>
> What you care most about is the relative energetics in vacuum; balancing
> intermolecular interactions is a totally separate issue.
>
> -Justin
>
>
>> On Fri, Mar 17, 2017 at 7:16
>> PM, <gromacs.org_gmx-users-request at maillist.sys.kth.se
>> <mailto:gromacs.org_gmx-users-request at maillist.sys.kth.se>> wrote:
>>
>> Message: 4
>> Date: Fri, 17 Mar 2017 09:45:21 -0400
>> From: Justin Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>> To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>> Subject: Re: [gmx-users] Dihedral drivers and 2D Energy Plot in
>> gromacs
>> Message-ID: <85061dd9-acaa-0b50-9eaf-4efb5081de64 at vt.edu
>> <mailto:85061dd9-acaa-0b50-9eaf-4efb5081de64 at vt.edu>>
>>
>> Content-Type: text/plain; charset=windows-1252; format=flowed
>>
>>
>>
>> On 3/17/17 1:40 AM, Devashish_Das wrote:
>> > Hello All,
>> >
>> > Presently we are working in generating dihedral drivers for AIB
>> dipeptide
>> > in gromacs. We would like to create energy contour maps for
>> different phi,
>> > psi angle for AIB in gromacs. We are unable to create the correct
>> energy
>> > map vs phi/psi angle of AIB dipeptide during energy minimization
>> step in
>> > Gromacs.
>> >
>> > Our MDP:
>> > #============================================================
>> > ; Parameters describing what to do, when to stop and what to save
>> > integrator = cg
>> > emtol = 1.0
>> > emstep = 0.01
>> > nsteps = 50000
>> > #============================================================
>> >
>> > We retraining the dihedral angles using the following method:
>> > http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints
>> <http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints>
>> (*Is this
>> > the correct way to do this?*)
>> >
>> > As clarified Dr Justin Lemkul in a private mail, we need to do the
>> > following:
>> >
>> > * The 2-D energy surface requires several steps. You need to
>> > assign dihedral restraints in the topology and relevant .mdp
>> options, and
>> > minimize the structures with those restrained phi/psi pairs. You
>> then need
>> > to deactivate the restraints and use mdrun -rerun to recompute the
>> energy
>> > of the minimized conformation to eliminate the contribution from the
>> > restraint potential
>> > (http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
>> <http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy>
>> > <http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
>> <http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy>>).
>> Then
>> > you need to offset the surface to the global minimum (done
>> completely
>> > outside GROMACS)*
>> >
>> > But we are having following trouble:
>> >
>> > a) "*You then need to deactivate the restraints and use mdrun
>> -rerun to
>> > recompute the energy of the minimized conformation to eliminate the
>> > contribution from the restraint potential*". How to do this? Which
>> .mdp
>> > file to be used for *mdrun -rerun*?
>> >
>>
>> Anything that's not energy minimization. Your topology also should
>> either not
>> include the dihedral restraint, or you should extract its
>> contribution from the
>> .edr file and subtract it from the total energy of the system.
>>
>> > b) "Then you need to offset the surface to the global minimum (done
>> > completely outside GROMACS)". Can you provide the required tool
>> name?
>> >
>>
>> There isn't one. This is a trivial scripting exercise. You assemble
>> the 2-D
>> matrix of energy values, find the lowest energy, and apply it as a
>> global offset
>> to all values.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> 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
>> <mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
>> <tel:%28410%29%20706-7441>
>> http://mackerell.umaryland.edu/~jalemkul
>> <http://mackerell.umaryland.edu/~jalemkul>
>>
>> ==================================================
>>
>>
>>
>> --
>>
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>> --
>>
>> Thanks & Regards,
>>
>> Devashish Das
>>
>>
>>
> --
> ==================================================
>
> 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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--
Regards,
Devashish Das
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