[gmx-users] Drude polarizable simulations
limingru
mruli at sina.com
Tue Oct 24 06:09:20 CEST 2017
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 have been using the gmx v4.6.5 to do something. I don't know if this version can run Drude polarizable simulations. 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!
--------------------------------
School of Nuclear Sci and Tec,
Beijing Normal University
Room.110,Teaching-Research Complex,
NO.10 WenHuiYuan St,Haiding District,
Beijing 100089,China
----- 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
> > --
> > Gromacs Users mailing list
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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
>>>> --
>>>> 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.
>>>>
>> --
>> 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.
>>
--
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.
------------------------------
Message: 3
Date: Mon, 23 Oct 2017 11:53:12 +0000
From: Mark Abraham <mark.j.abraham at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Conversion Amber to Gromacs
Message-ID:
<CAMNuMARwb80tDZWbKjxqaaPsWLR1DHBU8fcz+=EM09+wWzMJxw at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
On Mon, Oct 23, 2017 at 11:10 AM Elisa Pieri <elisa.pieri at univ-amu.fr>
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.
>
Chapter 2 of the reference manual describes the units. Chapter 4 describes
the functional forms, and e.g. tables in chapter 5 fill in the gaps. That
has always been enough for me when converting stuff to and from AMBER
descriptions.
Mark
> 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
> > >> --
> > >> 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.
> > >>
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
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> >
> --
> Gromacs Users mailing list
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> posting!
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------------------------------
Message: 4
Date: Mon, 23 Oct 2017 22:16:06 +0800
From: "limingru" <mruli at sina.com>
To: "gmx-users" <gmx-users at gromacs.org>
Subject: [gmx-users] Drude polarizable simulations
Message-ID: <20171023141606.3A4C081000EB at webmail.sinamail.sina.com.cn>
Content-Type: text/plain; charset=GBK
Dear gmx user,
How to carry out Drude polarizable simulations (Drude-2013 force field ) in GMX? whether it need to modify some parameters in certain force field, if possible, which files need to change? and how to get a itp file of SWM4-NDP? Thanks in advance.
------------------------------
Message: 5
Date: Mon, 23 Oct 2017 10:18:08 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Drude polarizable simulations
Message-ID: <556029d1-86fe-7f89-62c8-94a898ad981e at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
On 10/23/17 10:16 AM, limingru wrote:
> Dear gmx user,
> How to carry out Drude polarizable simulations (Drude-2013 force field ) in GMX? whether it need to modify some parameters in certain force field, if possible, which files need to change? and how to get a itp file of SWM4-NDP? Thanks in advance.
>
Example input files are in the SI of our 2015 JCC paper on the
implementation. All other force field files, etc are available from the
MacKerell lab website:
http://mackerell.umaryland.edu/charmm_drude_ff.shtml
Do not attempt to run simulations with domain decomposition; it is
currently broken. OpenMP parallelization works. We are nearing a fix (at
long last).
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
------------------------------
Message: 6
Date: Mon, 23 Oct 2017 22:39:25 +0530 (IST)
From: Varvdekar Bhagyesh Rajendra
<bhagyesh.varvdekar at research.iiit.ac.in>
To: gmx-users at gromacs.org
Subject: [gmx-users] Doubt about thermostat in MD
Message-ID:
<2004394973.1980727.1508778565679.JavaMail.zimbra at research.iiit.ac.in>
Content-Type: text/plain; charset=utf-8
Dear all,
I have to find vibrational spectrum of a protein-ligand complex in water using MD. Can anyone please suggest me what thermostats would be suited for NVT equilibration, NPT equilibration and MD production. I have read that for NVT, berendsen is suited while for NPT and MD part, nose-hoover is used.
Also, what constraints would be suited for finding vibrational spectrum. I plan to use all-H as constraints.
Thank you,
Bhagyesh
------------------------------
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