Re: [gmx-users] how to maintain planarity of graphene sheet

2016-01-15 Thread VITALY V. CHABAN 
I checked. They are from AMBER.



On Fri, Jan 15, 2016 at 5:50 AM, jagannath mondal 
wrote:

> Hi Vitaly
>
>   Unfortunately, the paper does not mention anything about whether the
> forcefields for graphene were taken from OPLS or AMBER.
> If I could get  the topology file  (even for part of) the graphene , it
> would have been  very helpful. I could have replicated and improvised the
> topology files for the graphene size I am interested in.
> Jagannath
>
> On Fri, Jan 15, 2016 at 6:14 AM, VITALY V. CHABAN 
> wrote:
>
>> The force constants were either from OPLS or from AMBER (which of these is
>> referenced in the paper?)
>>
>>
>>
>> On Thu, Jan 14, 2016 at 5:40 PM, jagannath mondal 
>> wrote:
>>
>> > Hi Vitaly
>> >   Thanks for pointing to the paper.
>> >   Based on the paper, "GR was simulated as a non-polarizable assembly of
>> > carbon atoms linked by harmonic potentials with the following bonded
>> > parameters: distance (C–C)= 1.41 nm, angle (C–C–C) = 120 , dihedral
>> (C–C–C
>> > –C) =0 "
>> >  Can you please specify what were the values of force-constant used for
>> > bonds, angle and dihedrals ?
>> > Jagannath
>> >
>> >
>> >
>> > On Thu, Jan 14, 2016 at 6:53 PM, VITALY V. CHABAN 
>> > wrote:
>> >
>> >> By using high force constants for all bonded terms.
>> >>
>> >> An ideally planar graphene in the solution/dispersion is an unphysical
>> >> model though. You must read literature for further insights:
>> >>
>> >>
>> >>
>> http://pubs.rsc.org/en/content/articlelanding/2015/ra/c5ra16857k#!divAbstract
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> On Thu, Jan 14, 2016 at 5:13 AM, jagannath mondal > >
>> >> wrote:
>> >>
>> >> > Hi
>> >> >
>> >> >   Which restraints can one  use to maintain planarity of graphene
>> sheets
>> >> > while performing MD simulations of their association ? I guess
>> >> > flat-bottommed restraints will not work.
>> >> >
>> >> > Jagannath
>> >> > --
>> >> > 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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>> or
>> >> > send a mail to gmx-users-requ...@gromacs.org.
>> >> >
>> >> --
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>> >
>> >
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>
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Re: [gmx-users] how to maintain planarity of graphene sheet

2016-01-14 Thread Justin Lemkul 



On 1/14/16 2:13 AM, jagannath mondal wrote:

Hi

   Which restraints can one  use to maintain planarity of graphene sheets
while performing MD simulations of their association ? I guess
flat-bottommed restraints will not work.



Planarity is governed by dihedrals, either proper, improper, or both, depending 
on the form of the force field.  If your simulations conditions lead to 
deformation, either the force field representation is wrong or whatever you're 
doing during the simulation is not physically sound.  Though, AFAIK graphene is 
not completely planar; some out-of-plane distortions are to be expected, as with 
any aromatic system.  The amplitude of that distortion is generally not large 
but is dependent upon whatever is going on in the simulation.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] how to maintain planarity of graphene sheet

2016-01-14 Thread VITALY V. CHABAN 
By using high force constants for all bonded terms.

An ideally planar graphene in the solution/dispersion is an unphysical
model though. You must read literature for further insights:

http://pubs.rsc.org/en/content/articlelanding/2015/ra/c5ra16857k#!divAbstract






On Thu, Jan 14, 2016 at 5:13 AM, jagannath mondal 
wrote:

> Hi
>
>   Which restraints can one  use to maintain planarity of graphene sheets
> while performing MD simulations of their association ? I guess
> flat-bottommed restraints will not work.
>
> Jagannath
> --
> 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
>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] how to maintain planarity of graphene sheet

2016-01-14 Thread VITALY V. CHABAN 
The force constants were either from OPLS or from AMBER (which of these is
referenced in the paper?)



On Thu, Jan 14, 2016 at 5:40 PM, jagannath mondal 
wrote:

> Hi Vitaly
>   Thanks for pointing to the paper.
>   Based on the paper, "GR was simulated as a non-polarizable assembly of
> carbon atoms linked by harmonic potentials with the following bonded
> parameters: distance (C–C)= 1.41 nm, angle (C–C–C) = 120 , dihedral (C–C–C
> –C) =0 "
>  Can you please specify what were the values of force-constant used for
> bonds, angle and dihedrals ?
> Jagannath
>
>
>
> On Thu, Jan 14, 2016 at 6:53 PM, VITALY V. CHABAN 
> wrote:
>
>> By using high force constants for all bonded terms.
>>
>> An ideally planar graphene in the solution/dispersion is an unphysical
>> model though. You must read literature for further insights:
>>
>>
>> http://pubs.rsc.org/en/content/articlelanding/2015/ra/c5ra16857k#!divAbstract
>>
>>
>>
>>
>>
>>
>> On Thu, Jan 14, 2016 at 5:13 AM, jagannath mondal 
>> wrote:
>>
>> > Hi
>> >
>> >   Which restraints can one  use to maintain planarity of graphene sheets
>> > while performing MD simulations of their association ? I guess
>> > flat-bottommed restraints will not work.
>> >
>> > Jagannath
>> > --
>> > 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-requ...@gromacs.org.
>> >
>> --
>> 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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>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
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Re: [gmx-users] how to maintain planarity of graphene sheet

2016-01-14 Thread jagannath mondal 
Hi Vitaly

  Unfortunately, the paper does not mention anything about whether the
forcefields for graphene were taken from OPLS or AMBER.
If I could get  the topology file  (even for part of) the graphene , it
would have been  very helpful. I could have replicated and improvised the
topology files for the graphene size I am interested in.
Jagannath

On Fri, Jan 15, 2016 at 6:14 AM, VITALY V. CHABAN 
wrote:

> The force constants were either from OPLS or from AMBER (which of these is
> referenced in the paper?)
>
>
>
> On Thu, Jan 14, 2016 at 5:40 PM, jagannath mondal 
> wrote:
>
> > Hi Vitaly
> >   Thanks for pointing to the paper.
> >   Based on the paper, "GR was simulated as a non-polarizable assembly of
> > carbon atoms linked by harmonic potentials with the following bonded
> > parameters: distance (C–C)= 1.41 nm, angle (C–C–C) = 120 , dihedral
> (C–C–C
> > –C) =0 "
> >  Can you please specify what were the values of force-constant used for
> > bonds, angle and dihedrals ?
> > Jagannath
> >
> >
> >
> > On Thu, Jan 14, 2016 at 6:53 PM, VITALY V. CHABAN 
> > wrote:
> >
> >> By using high force constants for all bonded terms.
> >>
> >> An ideally planar graphene in the solution/dispersion is an unphysical
> >> model though. You must read literature for further insights:
> >>
> >>
> >>
> http://pubs.rsc.org/en/content/articlelanding/2015/ra/c5ra16857k#!divAbstract
> >>
> >>
> >>
> >>
> >>
> >>
> >> On Thu, Jan 14, 2016 at 5:13 AM, jagannath mondal 
> >> wrote:
> >>
> >> > Hi
> >> >
> >> >   Which restraints can one  use to maintain planarity of graphene
> sheets
> >> > while performing MD simulations of their association ? I guess
> >> > flat-bottommed restraints will not work.
> >> >
> >> > Jagannath
> >> > --
> >> > 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-requ...@gromacs.org.
> >> >
> >> --
> >> 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-requ...@gromacs.org.
> >>
> >
> >
> --
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>
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