[gmx-users] DPD in Groamcs
praveen kumar
praveenche at gmail.com
Wed Oct 25 06:54:52 CEST 2017
Thanks alot Goga N and Raman Preet Singh,
I have to simulate the polymer thin film of the order of sub nanometer
length scale, though I have gone through the DPDMacs, am able to run simple
DPD calculations, but haven't found any reference article that used
DPD-MACS. In addition to that we cannot simply calculate any thermodynamic
properties like Delta_G and Delta_H, using DPDMACS. As Gromcs Approach of
free-enrgy calculation we cannot simply implement to It. I hope this would
topic of future interest those who want to develop.
However most of the references i have found either uses LAMMPS, DL_Meso and
Mesodyn. But post procssing needs to be coded on their own,I hope we should
go ahead with well tested LAMMPS.
Best
Praveen
On Tue, Oct 24, 2017 at 7:01 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Contact map (spss4 at iacs.res.in)
> 2. Re: DPD in Groamcs (Raman Preet Singh)
> 3. Re: DPD in Groamcs (Raman Preet Singh)
> 4. Re: DPD in Groamcs (Goga, N.)
> 5. (no subject) (limingru)
> 6. Re: Drude polarizable simulations (Justin Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 24 Oct 2017 17:28:38 +0530
> From: spss4 at iacs.res.in
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Contact map
> Message-ID:
> <20171024172838.Horde.DkOZH3IrO8Jn-6CHOd0WnA1 at mailweb.iacs.res.in>
> Content-Type: text/plain; charset=UTF-8; format=flowed; DelSp=Yes
>
> Hi all
> I want to generate a contact map for all the residues of lysozyme protein.
> I am using gmx mdmat to generate this. Can I generate a text file (which
> can be open in Grace) except the image files(eg: xpm file)? Please let me
> know the particular flag which I can use to get a *.xvg file.
>
> Thanks
> Sunipa Sarkar
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 24 Oct 2017 12:27:09 +0000
> From: Raman Preet Singh <ramanpreetsingh at hotmail.com>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] DPD in Groamcs
> Message-ID:
> <MA1PR01MB02647E33FAB041CD06BBDE45B3470 at MA1PR01MB0264.
> INDPRD01.PROD.OUTLOOK.COM>
>
> Content-Type: text/plain; charset="utf-8"
>
> I was looking for DPD in Gromacs too but in vain. You may try DPDmacs,
> POLY DL or LAMPPS.
>
> ------------------------------
>
> Message: 3
> Date: Tue, 24 Oct 2017 12:32:19 +0000
> From: Raman Preet Singh <ramanpreetsingh at hotmail.com>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] DPD in Groamcs
> Message-ID:
> <MA1PR01MB0264F0C6F85A00769FD6F566B3470 at MA1PR01MB0264.
> INDPRD01.PROD.OUTLOOK.COM>
>
> Content-Type: text/plain; charset="utf-8"
>
> Forgot to mention Materials Studio..... An extremely easy-to-use software
> but comes at a hefty license fee.
>
> On Oct 24, 2017 5:57 PM, Raman Preet Singh <ramanpreetsingh at hotmail.com<
> mailto:ramanpreetsingh at hotmail.com>> wrote:
>
> I was looking for DPD in Gromacs too but in vain. You may try DPDmacs,
> POLY DL or LAMPPS.
>
> ------------------------------
>
> Message: 4
> Date: Tue, 24 Oct 2017 15:30:34 +0300
> From: "Goga, N." <n.goga at rug.nl>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] DPD in Groamcs
> Message-ID:
> <CAAHQ6H4=7g0d1ucJY_qAUg62v_tUYT3OtYqP+HZQdtMreEWikg at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Friend,
>
> I may have some older version of DPD-gromacs. However, I am not sure for
> what you need it. Being trial, that version might not be completely free of
> errors.
>
> Nicu
>
> On Tue, Oct 24, 2017 at 3:27 PM, Raman Preet Singh <
> ramanpreetsingh at hotmail.com> wrote:
>
> > I was looking for DPD in Gromacs too but in vain. You may try DPDmacs,
> > POLY DL or LAMPPS.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
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> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 24 Oct 2017 21:24:28 +0800
> From: "limingru" <mruli at sina.com>
> To: "gmx-users" <gmx-users at gromacs.org>
> Subject: [gmx-users] (no subject)
> Message-ID: <20171024132428.DFB3381000EB at webmail.sinamail.sina.com.cn>
> Content-Type: text/plain; charset=GBK
>
> Dear all, I want to use GMX to simulate ethanol solution
> interaction with macromolecular in a polarizable force filed. Whether the
> macromolecular and ethanol PDB files need adding Drude particles? and how
> to produce an ethanol.itp file for Drude2013 force field? Do the Drude2013
> force field can be ran in the GMX v4.6.5? Thanks in advance.
> 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
>
>
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 24 Oct 2017 09:31:36 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Drude polarizable simulations
> Message-ID: <e6050f19-1d1f-d3a3-2a89-0b0acfbcda06 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> 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!
> > --------------------------------
> >
> >
> > 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
> >
> >
> > Send gromacs.org_gmx-users mailing list submissions to
> > gromacs.org_gmx-users at maillist.sys.kth.se
> > To subscribe or unsubscribe via the World Wide Web, visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or, via email, send a message with subject or body 'help' to
> > gromacs.org_gmx-users-request at maillist.sys.kth.se
> > You can reach the person managing the list at
> > gromacs.org_gmx-users-owner at maillist.sys.kth.se
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of gromacs.org_gmx-users digest..."
> > 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
> >>>
> >>> * 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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> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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> >> send a mail to gmx-users-request at gromacs.org.
> >>
> > ------------------------------
> > 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
> >>>
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> >>>
>
> --
> ==================================================
>
> 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
>
> ==================================================
>
>
>
> ------------------------------
>
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> End of gromacs.org_gmx-users Digest, Vol 162, Issue 91
> ******************************************************
>
--
Thanks & Regards
Dr.Praveen Kumar Sappidi,
National Post Doctoral Fellow.
Computational Nanoscience Laboratory,
Chemical Engineering Department,
IIT Kanpur,India-208016
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