[gmx-users] Drude polarizable simulations

Justin Lemkul jalemkul at vt.edu
Tue Oct 24 15:31:49 CEST 2017 


On 10/24/17 12:08 AM, limingru wrote:
> Hello Justin,			Many thanks for your answer. Another question is that whether I need adding some Drude particles in my PDB file of DNA or Protein in the simulation process, if any, how to modify the PDB file?  I

pdb2gmx will build everything for you.

> have been using the gmx v4.6.5 to do something. I don't know if this version can run Drude polarizable simulations.

No, you need to check out the developmental version of the code and use 
the Drude branch.

-Justin

> I am going to do protein interaction with organic solution (e.g. ethanol or methanol, etc) in Drude2013 force filed using gromacs software. Would you please give me some warnings? I think it will give me more clear direction and bring me convenience in simulation process. Thanks a lot.
> 		Best wishes!
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> Beijing Normal University
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> ----- Original Message -----
> From: gromacs.org_gmx-users-request at maillist.sys.kth.se
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: gromacs.org_gmx-users Digest, Vol 162, Issue 88
> Date: 2017-10-24 01:10
>
>
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> Today's Topics:
>     1. Re: DPD in Groamcs (Goga, N.)
>     2. Re: Conversion Amber to Gromacs (Thomas Piggot)
>     3. Re: Conversion Amber to Gromacs (Mark Abraham)
>     4. Drude polarizable simulations (limingru)
>     5. Re: Drude polarizable simulations (Justin Lemkul)
>     6. Doubt about thermostat in MD (Varvdekar Bhagyesh Rajendra)
> ----------------------------------------------------------------------
> Message: 1
> Date: Mon, 23 Oct 2017 13:54:20 +0300
> From: "Goga, N." <n.goga at rug.nl>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] DPD in Groamcs
> Message-ID:
> 	<CAAHQ6H62djzjnd=pJzUSCzz9GVFu9Gxtk32yCotdjgCPCisErA at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
> Dear Kumar,
> Why do you need DPD?
> Nicu
> On Sun, Oct 22, 2017 at 11:28 PM, Dallas Warren <dallas.warren at monash.edu>
> wrote:
>> Not directly, though one of developers might have better insight into
>> that.  Though there are requests / proposals to add it
>> https://redmine.gromacs.org/issues/1885
>>
>> There is DPDmacs http://www.apmaths.uwo.ca/~mkarttu/dpdmacs.shtml
>> Catch ya,
>>
>> Dr. Dallas Warren
>> Drug Delivery, Disposition and Dynamics
>> Monash Institute of Pharmaceutical Sciences, Monash University
>> 381 Royal Parade, Parkville VIC 3052
>> dallas.warren at monash.edu
>> ---------------------------------
>> When the only tool you own is a hammer, every problem begins to resemble a
>> nail.
>>
>>
>> On 21 October 2017 at 23:53, praveen kumar <praveenche at gmail.com> wrote:
>>> Dear all
>>> is there any possibility of  performing dissipative particle dynamics
>> (DPD)
>>> in gromacs?
>>>
>>> Thanks in Advance
>>> Praveen
>>> --
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> ------------------------------
> Message: 2
> Date: Mon, 23 Oct 2017 12:13:14 +0100
> From: Thomas Piggot <t.piggot at soton.ac.uk>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Conversion Amber to Gromacs
> Message-ID: <afca89bc-2553-90d1-b2ab-009a4e819f07 at soton.ac.uk>
> Content-Type: text/plain; charset=utf-8; format=flowed
> Hi,
> The multiplicity/periodicity is the same but always positive in GROMACS.
> Kd in GROMACS is the AMBER value multiplied by 4.184 then divided by
> IDIVF (the entry after names in AMBER file). The phase is the same.
> For more info on why see ambermd.org/formats.html#parm.dat
> Cheers
> Tom
> On 23/10/17 10:09, Elisa Pieri wrote:
>> Hello again,
>>
>> sorry I wasn't very clear perhaps..we are trying to modify directly the
>> ffbonded.itp file (together with all the other interested ones) in the
>> Amber94 force field in order to include the Amber Lipids17 force field. We
>> added most of the parameters with no problems (bond equilibrium lengths,
>> constants, bending and so on), but we were not able to understand what is
>> the conversion factor for torsion parameters between the Amber software
>> Suite and Gromacs. I know that in the Amber package, the dihedral force
>> constant is expressed in Kcal/mol, but I couldn't understand what are the
>> units (and therefore how to convert the parameters) in Gromacs.
>>
>> Any idea?
>> Elisa
>>
>> On Fri, Oct 20, 2017 at 7:17 PM, p.kartheek <kartheekpitta at gmail.com> wrote:
>>
>>> ParmEd (https://parmed.github.io/ParmEd/html/parmed.html) would be the
>>> appropriate software for converting topologies.
>>> This is the parm.py  script I have employed, supply amber topologies
>>> file.prmtop and file.inpcrd as input and amber.save option will give
>>> converted gromacs topologies as output.
>>>
>>> import parmed as pmd
>>> #amber = pmd.load_file('prmtop', 'inpcrd')
>>> amber = pmd.load_file('new24_ang.prmtop', 'new24_ang.inpcrd')
>>> #save a GROMACS topology and GRO file
>>> amber.save('new24_ang.top')
>>> amber.save('new24_ang.gro')
>>>
>>>
>>> ----------------------------------------------
>>> P. Kartheek,
>>> PhD Candidate, Computational Biophysical Chemistry,
>>> Center for Computational Natural Sciences and Bioinformatics,
>>> International Institute of Information Technology,
>>> Marimuthu Krishan Group,
>>> 9701577399,
>>> kartheek.p at research.iiit.ac.in,
>>>
>>>
>>> On Fri, Oct 20, 2017 at 10:30 PM, p.kartheek <kartheekpitta at gmail.com>
>>> wrote:
>>>
>>>> You can do with ParmEd
>>>> On Oct 20, 2017 10:07 PM, "Elisa Pieri" <elisa.pieri at univ-amu.fr> wrote:
>>>>
>>>>> Hello GMX users/developers,
>>>>>
>>>>> we are trying to add the Amber lipids17 forcefield to the Amber99
>>>>> forcefield implemented in Gromacs. We are a little bit lost on the
>>> torsion
>>>>> parameters: how to convert the constant from Amber to Gromacs?
>>>>>
>>>>> Thank you in advance!
>>>>> Elisa
>>>>> --
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>>>>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
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