charmm forcefield

hi every body

my system includes zeolite (inorganic polymer ) and protein .
I want to use charmm ff.
can I use ch2lmp tool to convert whole of my system in charmm ff??
or should I part my system in two ( protein and polymer ) to convert?

thanks in advance
ramin


|

hi every body

my system includes zeolite (inorganic polymer ) and protein .
I want to use charmm ff.
can I use ch2lmp tool to convert whole of my system in charmm ff??

do you have CHARMM compatible parameters for your zeolithe?
and mixed terms describing how those atoms interact with your
protein? *that* is the key question, not how to use chm2lmp.

axel.

yes par_silicates charmm ff includes zeolite parameters almost.
and **par_all22_prot charmm ff ** includes my protein parameters.

ramin

— On Tue, 6/19/12, Axel Kohlmeyer [email protected] wrote:


> From: Axel Kohlmeyer [email protected]
> Subject: Re: [lammps-users] charmm forcefield
> To: “Ramin Ekhteiari” <[email protected]…16…>
> Cc: [email protected]
> Date: Tuesday, June 19, 2012, 7:42 PM
>
> On Tue, Jun 19, 2012 at 3:31 PM, Ramin Ekhteiari <[email protected]…16…> wrote:
> >
> > hi every body
> >
> > my system includes zeolite (inorganic polymer ) and protein .
> > I want to use charmm ff.
> > can I use ch2lmp tool to convert whole of my system in charmm ff??
>
> do you have CHARMM compatible parameters for your zeolithe?
> and mixed terms describing how those atoms interact with your
> protein? that is the key question, not how to use chm2lmp.
>
> axel.
>
> > or should I part my system in two ( protein and polymer ) to convert?
> >
> > thanks in advance
> > ramin
> >
> >
> >
> >
> > ------------------------------------------------------------------------------
> > Live Security Virtual Conference
> > Exclusive live event will cover all the ways today’s security and
> > threat landscape has changed and how IT managers can respond. Discussions
> > will include endpoint security, mobile security and the latest in malware
> > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> > _______________________________________________
> > lammps-users mailing list
> > [email protected]
> > https://lists.sourceforge.net/lists/listinfo/lammps-users
> >
>
> –
> Dr. Axel Kohlmeyer
> [email protected] http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.

|

yes **par_silicates charmm ff** includes zeolite parameters almost.
and **par_all22_prot charmm ff ** includes my protein parameters.

well, that doesn't mean you have good
parameters for the interactions between the two.

the parameters generated from using mixing
rules are not likely to be very good and would
need NBFIX entries.

axel.

what do you mean by NBFIX entries ?

ramin

— On Wed, 6/20/12, Axel Kohlmeyer [email protected] wrote:


> From: Axel Kohlmeyer [email protected]
> Subject: Re: [lammps-users] charmm forcefield
> To: “Ramin Ekhteiari” <[email protected]…16…>
> Cc: [email protected]…396…sourceforge.net
> Date: Wednesday, June 20, 2012, 11:37 AM
>
> On Wed, Jun 20, 2012 at 7:22 AM, Ramin Ekhteiari <[email protected]…16…> wrote:
> >
> > yes par_silicates charmm ff includes zeolite parameters almost.
> > and **par_all22_prot charmm ff ** includes my protein parameters.
>
> well, that doesn’t mean you have good
> parameters for the interactions between the two.
>
> the parameters generated from using mixing
> rules are not likely to be very good and would
> need NBFIX entries.
>
> axel.
>
> >
> > ramin
> >
> > — On Tue, 6/19/12, Axel Kohlmeyer <[email protected]…36…24…> wrote:
> >
> >
> > From: Axel Kohlmeyer [email protected]
> > Subject: Re: [lammps-users] charmm forcefield
> > To: “Ramin Ekhteiari” <[email protected]…16…>
> > Cc: [email protected]
> > Date: Tuesday, June 19, 2012, 7:42 PM
> >
> >
> > On Tue, Jun 19, 2012 at 3:31 PM, Ramin Ekhteiari <[email protected]…16…>
> > wrote:
> > >
> > > hi every body
> > >
> > > my system includes zeolite (inorganic polymer ) and protein .
> > > I want to use charmm ff.
> > > can I use ch2lmp tool to convert whole of my system in charmm ff??
> >
> > do you have CHARMM compatible parameters for your zeolithe?
> > and mixed terms describing how those atoms interact with your
> > protein? that is the key question, not how to use chm2lmp.
> >
> > axel.
> >
> >
> > > or should I part my system in two ( protein and polymer ) to convert?
> > >
> > > thanks in advance
> > > ramin
> > >
> > >
> > >
> > >
> > >
> > > ------------------------------------------------------------------------------
> > > Live Security Virtual Conference
> > > Exclusive live event will cover all the ways today’s security and
> > > threat landscape has changed and how IT managers can respond.
> > > Discussions
> > > will include endpoint security, mobile security and the latest in
> > > malware
> > > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> > > _______________________________________________
> > > lammps-users mailing list
> > > [email protected]…44…s.sourceforge.net
> > > https://lists.sourceforge.net/lists/listinfo/lammps-users
> > >
> >
> >
> >
> > –
> > Dr. Axel Kohlmeyer
> > [email protected] http://goo.gl/1wk0
> >
> > College of Science and Technology
> > Temple University, Philadelphia PA, USA.
>
> –
> Dr. Axel Kohlmeyer
> [email protected] http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.

|

NBFIX are overrides for nonbonded parameters where regular mixing does not work well. Please read the documentation of the charmm forcefield and the respective publications. It is a bad idea to blindly use a force field.

Axel