[gmx-users] Charmm27 and Charmm36 atomtypes assignments for polymer
Mijiddorj B
b.mijiddorj at gmail.com
Thu Nov 21 09:59:57 CET 2019
Dear Justin,
Thank you very much for your kind advice. I see.
Best regards,
Mijiddorj
--------------------------
>
> Message: 3
> Date: Wed, 20 Nov 2019 20:56:58 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Charmm27 and Charmm36 atomtypes assignments
> for polymer
> Message-ID: <b804ac29-633b-6932-f92c-ab372e7b1585 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/20/19 8:51 PM, Mijiddorj B wrote:
> > Dear Prof. Justin,
> >
> > Thank you very much for your reply. I would like to use charmm27 because
> my
> > system contains a surface model, which were parametrized by INTERFACE
> Force
> > Field and compatible with charmm27. The polymer parameters of charmm27
> were
>
> AFAIK there's no reason to believe you have to use CHARMM27; INTERFACE
> is generally compatible with CHARMM, which has a linear development
> history so you should be able to combine it with any CHARMM potential.
>
> > generated by swissparam, and the server renamed the atomtypes. I would
> like
> > to assign those parameters with original charmm27. If possible, I would
> > like to use original charmm27 parameters instead of the values of
> > swissparam. I used charmm36 atomtypes for clarification.
> > I do not know the atom type of the nitrogen which connected with three
> > carbons.
>
> NG301. I still think it's best if you simply parametrize your monomer
> units with CGenFF and use its parameters unless there are major penalties.
>
> -Justin
>
> >
> > Best regards,
> >
> > Mijiddorj
> >
> > ------------------------------
> >> Message: 5
> >> Date: Wed, 20 Nov 2019 20:19:16 -0500
> >> From: Justin Lemkul <jalemkul at vt.edu>
> >> To: gmx-users at gromacs.org
> >> Subject: Re: [gmx-users] Charmm27 and Charmm36 atomtypes assignments
> >> for polymer
> >> Message-ID: <7db2548d-f487-a34b-f27f-0f876aa202ca at vt.edu>
> >> Content-Type: text/plain; charset=utf-8; format=flowed
> >>
> >>
> >>
> >> On 11/19/19 9:54 PM, Mijiddorj B wrote:
> >>> Dear Gmx users,
> >>>
> >>> Currently, I am trying to assign the atomtypes in charmm27 for the
> >>> polyethyleneimine polymer. It includes several different groups of
> >> atoms. I
> >>> included following illustration and asignment:
> >>> ##############################################
> >>> H CH2
> >>> | /
> >>> NH2--CH2--CH2--N--CH2--CH2--N--CH2 ...
> >>>
> >>> ##############################################
> >>> I assigned and the charmm27 atomtypes as following and compared
> charmm36
> >>> atomtypes generated by CgenFF.
> >>> Atom Charmm27 Charmm36
> >>> N (NH2) ---> NH2 | NG321
> >>> N (NH1) ---> NH1 | NG311
> >>> C (CH2) ---> CT2 | CG321
> >>> H (HC2) ---> HA | HGA2
> >>> N ? | NG301
> >>>
> >>> If you have any experience, please check my assignments the charmm27
> atom
> >>> types and advice me the atomtype of the last Nitrogen, which were
> >> assigned
> >>> as NG301 with CgenFF.
> >> Why are you replacing the CGenFF atom types? The replacements you are
> >> making completely change the LJ terms and therefore render the dihedral
> >> parameters invalid. There is no need to make these changes, just use the
> >> CGenFF atom types in your simulation (all of which is contained in the
> >> CHARMM36 port, which you should use rather than the outdated CHARMM27
> >> force field files).
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
> >>
> >>
> >> ------------------------------
> >>
> >> --
> >> Gromacs Users mailing list
> >>
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> >>
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> >>
> >> End of gromacs.org_gmx-users Digest, Vol 187, Issue 49
> >> ******************************************************
> >>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 21 Nov 2019 08:40:08 +0100
> From: Alessandra Villa <alessandra.villa.biosim at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Chain length of a polymer
> Message-ID:
> <
> CANogp5zuHNcfssKrTUDNDSsT3WxDT22PzxSjwCn7War+-M8n2A at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> I understood, that you would like to monitor the distance between the two
> ends of your chains along the simulation. If this is the case
> you could use
> gmx distance (see
> http://manual.gromacs.org/current/onlinehelp/gmx-distance.html) together
> with the appropriate selection (e.i. you could calculate the distance
> between the com of the two polymer ends)
> In alternative you can use gmx mindist (
> http://manual.gromacs.org/2019/onlinehelp/gmx-mindist.html)
>
> To generate index files you can use gmx make_ndx (
> http://manual.gromacs.org/2019/onlinehelp/gmx-make_ndx.html)
>
> Best regards
> Alessandra
>
> On Thu, Nov 21, 2019 at 1:40 AM Shan Jayasinghe <
> shanjayasinghe2011 at gmail.com> wrote:
>
> > Dear Gromacs Users,
> >
> > I have a polymer molecule in my MD simulation and I want to calculate how
> > chain length varies with simulation time. How can I do that with Gromacs
> > software? Can I use gmx distance? Do I need to create a group with
> backbone
> > atoms of the polymer chain in the index file for the calculation?
> > Appreciate your help.
> >
> > Thank you.
> > --
> > Best Regards
> > Shan Jayasinghe
> > --
> > 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.
> >
>
>
>
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