[gmx-users] Dihedral drivers and 2D Energy Plot in gromacs
Justin Lemkul
jalemkul at vt.edu
Wed Mar 22 00:07:10 CET 2017
On 3/21/17 7:02 PM, Devashish_Das wrote:
> 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?
>
You shouldn't be doing the calculations in water at all. From our previous
conversation, I understood that you wanted a 2-D energy plot as a function of
(phi,psi) for AIB. You do that in vacuo. That gives you the relative
conformational energy of the peptide as a function of the backbone geometry.
You can then look at the sampling during an MD simulation to see where the
configurations lie on that energy surface to understand if hydration causes a
shift in the sampling from the "intrinsic" state.
-Justin
> 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>
>>>
>>> ==================================================
>>>
>>>
>>>
>>> --
>>>
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive
>>> at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
>>> <http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> <http://www.gromacs.org/Support/Mailing_Lists>
>>>
>>> * For (un)subscribe requests visit
>>>
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>> <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>
>>> or send
>>> a mail to gmx-users-request at gromacs.org <mailto:
>>> gmx-users-request at gromacs.org>.
>>>
>>>
>>> --
>>>
>>> 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
>>
>> ==================================================
>> --
>> 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-request at gromacs.org.
>>
>
>
>
--
==================================================
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
==================================================
More information about the gromacs.org_gmx-users
mailing list