Re: [gmx-users] virtual site connected to dummy massive site

[Mark Abraham]

Hi,

Your linear version has two rotation axes (and thus DOF) because it has
mass distribution. Your point version has no mass distribution.

Mark

On Sun, Nov 26, 2017 at 7:52 PM Faezeh Pousaneh  wrote:

> Please note that the carbon is a virtual site, so has not mass. So the DOF
> does not influence of its configurations on average. Besides the angle   of
> M--C--M is always 180.
>
> Mark, I compare the results of average distributions not a snapshot.
>
> Justin, the only LJ are from atom C with next molecules in both systems.
> (In fact I got the idea from your carbon dioxide tutorial, in which later I
> will add two more virtual sites with charges to create a dipole moment for
> my atom (e.g C here), but first I must understand this stage)
>
>
>
> Best regards
>
>
> On Sun, Nov 26, 2017 at 7:12 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > On Sun, Nov 26, 2017 at 6:35 PM Faezeh Pousaneh 
> > wrote:
> >
> > > Hi Mark, sorry I am not convinced yet. I hope you did not misunderstand
> > my
> > > question, I have no charges in systems on any atoms. So the extra DOF
> do
> > > not effect on potential.
> > >
> >
> > Charge has nothing to do with it. The potential is computed from all the
> > interactions in the system, which in your case includes LJ. You aren't
> > going to generate the same ensemble of configurations in your two cases,
> so
> > you cannot expect to observe the same distribution of potential energy.
> >
> > Note that it would have been nice to say whether you were comparing a
> > distribution of energies or a snapshot. As it is, we are guessing.
> >
> > Mark
> >
> > Best regards
> > >
> > >
> > > On Fri, Nov 24, 2017 at 11:03 AM, Mark Abraham <
> mark.j.abra...@gmail.com
> > >
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > Potential energy is a function of configuration. You can expect the
> > same
> > > LJ
> > > > energy if you compare the same configuration, ie that the
> distribution
> > of
> > > > states is identical. But if you would have the same total energy and
> a
> > > > different distribution between PE and KE (because the DOF change)
> then
> > > you
> > > > will not sample the same states.
> > > >
> > > > Mark
> > > >
> > > > On Fri, Nov 24, 2017 at 10:56 AM Faezeh Pousaneh <
> fpoosa...@gmail.com>
> > > > wrote:
> > > >
> > > > > Dear Mark,
> > > > > thanks, but degrees of freedom goes to kinetic energies, still LJ
> > > > energies
> > > > > must be the same, yes?
> > > > >
> > > > >
> > > > > Best regards
> > > > >
> > > > >
> > > > > On Fri, Nov 24, 2017 at 8:22 AM, Mark Abraham <
> > > mark.j.abra...@gmail.com>
> > > > > wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > Your systems have different available degrees of freedom, so they
> > > > sample
> > > > > > difference spaces. The energies you observe reflect that
> > difference.
> > > > > >
> > > > > > Mark
> > > > > >
> > > > > > On Mon, 20 Nov 2017 18:18 Faezeh Pousaneh 
> > > wrote:
> > > > > >
> > > > > > > Hi,
> > > > > > >
> > > > > > > I have a system containing of a virtual site of carbon
> connected
> > > > > > > symmetrically to two dummy massive sites (no charge). like :
> > > > M---C---M
> > > > > > > My problem is the results I get from simulation of this system
> is
> > > not
> > > > > > equal
> > > > > > > with results of single Carbon system simulation with mass of 2M
> > (at
> > > > > > exactly
> > > > > > > similar conditions)?
> > > > > > > They produce different LJ coul energies, I have even tried for
> > > > > > non-charged
> > > > > > > systems.
> > > > > > >
> > > > > > > Thank you in advance for help,
> > > > > > > Best regards
> > > > > > > --
> > > > > > > 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.
> > > > > > >
> > > > > > --
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> > > > > >
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> > > > > posting!
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> > > > > * Can't post? Read 

Re: [gmx-users] virtual site connected to dummy massive site

[Faezeh Pousaneh]

Please note that the carbon is a virtual site, so has not mass. So the DOF
does not influence of its configurations on average. Besides the angle   of
M--C--M is always 180.

Mark, I compare the results of average distributions not a snapshot.

Justin, the only LJ are from atom C with next molecules in both systems.
(In fact I got the idea from your carbon dioxide tutorial, in which later I
will add two more virtual sites with charges to create a dipole moment for
my atom (e.g C here), but first I must understand this stage)



Best regards


On Sun, Nov 26, 2017 at 7:12 PM, Mark Abraham 
wrote:

> Hi,
>
> On Sun, Nov 26, 2017 at 6:35 PM Faezeh Pousaneh 
> wrote:
>
> > Hi Mark, sorry I am not convinced yet. I hope you did not misunderstand
> my
> > question, I have no charges in systems on any atoms. So the extra DOF do
> > not effect on potential.
> >
>
> Charge has nothing to do with it. The potential is computed from all the
> interactions in the system, which in your case includes LJ. You aren't
> going to generate the same ensemble of configurations in your two cases, so
> you cannot expect to observe the same distribution of potential energy.
>
> Note that it would have been nice to say whether you were comparing a
> distribution of energies or a snapshot. As it is, we are guessing.
>
> Mark
>
> Best regards
> >
> >
> > On Fri, Nov 24, 2017 at 11:03 AM, Mark Abraham  >
> > wrote:
> >
> > > Hi,
> > >
> > > Potential energy is a function of configuration. You can expect the
> same
> > LJ
> > > energy if you compare the same configuration, ie that the distribution
> of
> > > states is identical. But if you would have the same total energy and a
> > > different distribution between PE and KE (because the DOF change) then
> > you
> > > will not sample the same states.
> > >
> > > Mark
> > >
> > > On Fri, Nov 24, 2017 at 10:56 AM Faezeh Pousaneh 
> > > wrote:
> > >
> > > > Dear Mark,
> > > > thanks, but degrees of freedom goes to kinetic energies, still LJ
> > > energies
> > > > must be the same, yes?
> > > >
> > > >
> > > > Best regards
> > > >
> > > >
> > > > On Fri, Nov 24, 2017 at 8:22 AM, Mark Abraham <
> > mark.j.abra...@gmail.com>
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > Your systems have different available degrees of freedom, so they
> > > sample
> > > > > difference spaces. The energies you observe reflect that
> difference.
> > > > >
> > > > > Mark
> > > > >
> > > > > On Mon, 20 Nov 2017 18:18 Faezeh Pousaneh 
> > wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > I have a system containing of a virtual site of carbon connected
> > > > > > symmetrically to two dummy massive sites (no charge). like :
> > > M---C---M
> > > > > > My problem is the results I get from simulation of this system is
> > not
> > > > > equal
> > > > > > with results of single Carbon system simulation with mass of 2M
> (at
> > > > > exactly
> > > > > > similar conditions)?
> > > > > > They produce different LJ coul energies, I have even tried for
> > > > > non-charged
> > > > > > systems.
> > > > > >
> > > > > > Thank you in advance for help,
> > > > > > Best regards
> > > > > > --
> > > > > > 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
> > > > >
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> > > > > Support/Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] virtual site connected to dummy massive site

[Mark Abraham]

Hi,

On Sun, Nov 26, 2017 at 6:35 PM Faezeh Pousaneh  wrote:

> Hi Mark, sorry I am not convinced yet. I hope you did not misunderstand my
> question, I have no charges in systems on any atoms. So the extra DOF do
> not effect on potential.
>

Charge has nothing to do with it. The potential is computed from all the
interactions in the system, which in your case includes LJ. You aren't
going to generate the same ensemble of configurations in your two cases, so
you cannot expect to observe the same distribution of potential energy.

Note that it would have been nice to say whether you were comparing a
distribution of energies or a snapshot. As it is, we are guessing.

Mark

Best regards
>
>
> On Fri, Nov 24, 2017 at 11:03 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Potential energy is a function of configuration. You can expect the same
> LJ
> > energy if you compare the same configuration, ie that the distribution of
> > states is identical. But if you would have the same total energy and a
> > different distribution between PE and KE (because the DOF change) then
> you
> > will not sample the same states.
> >
> > Mark
> >
> > On Fri, Nov 24, 2017 at 10:56 AM Faezeh Pousaneh 
> > wrote:
> >
> > > Dear Mark,
> > > thanks, but degrees of freedom goes to kinetic energies, still LJ
> > energies
> > > must be the same, yes?
> > >
> > >
> > > Best regards
> > >
> > >
> > > On Fri, Nov 24, 2017 at 8:22 AM, Mark Abraham <
> mark.j.abra...@gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > Your systems have different available degrees of freedom, so they
> > sample
> > > > difference spaces. The energies you observe reflect that difference.
> > > >
> > > > Mark
> > > >
> > > > On Mon, 20 Nov 2017 18:18 Faezeh Pousaneh 
> wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > I have a system containing of a virtual site of carbon connected
> > > > > symmetrically to two dummy massive sites (no charge). like :
> > M---C---M
> > > > > My problem is the results I get from simulation of this system is
> not
> > > > equal
> > > > > with results of single Carbon system simulation with mass of 2M (at
> > > > exactly
> > > > > similar conditions)?
> > > > > They produce different LJ coul energies, I have even tried for
> > > > non-charged
> > > > > systems.
> > > > >
> > > > > Thank you in advance for help,
> > > > > Best regards
> > > > > --
> > > > > 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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Re: [gmx-users] virtual site connected to dummy massive site

[Justin Lemkul]

On 11/26/17 12:34 PM, Faezeh Pousaneh wrote:

Hi Mark, sorry I am not convinced yet. I hope you did not misunderstand my
question, I have no charges in systems on any atoms. So the extra DOF do
not effect on potential.


Maybe I (and others) are missing something here. We understand there are 
no charges, but that only affects the Coulombic energies. The LJ 
potentials of two systems are only the same if the interacting species 
have the same configuration. Do your virtual particles interact with 
anything via LJ? If they don't, I don't understand their purpose. You 
have to do an apples-to-apples comparison.


-Justin



Best regards


On Fri, Nov 24, 2017 at 11:03 AM, Mark Abraham 
wrote:


Hi,

Potential energy is a function of configuration. You can expect the same LJ
energy if you compare the same configuration, ie that the distribution of
states is identical. But if you would have the same total energy and a
different distribution between PE and KE (because the DOF change) then you
will not sample the same states.

Mark

On Fri, Nov 24, 2017 at 10:56 AM Faezeh Pousaneh 
wrote:


Dear Mark,
thanks, but degrees of freedom goes to kinetic energies, still LJ

energies

must be the same, yes?


Best regards


On Fri, Nov 24, 2017 at 8:22 AM, Mark Abraham 
wrote:


Hi,

Your systems have different available degrees of freedom, so they

sample

difference spaces. The energies you observe reflect that difference.

Mark

On Mon, 20 Nov 2017 18:18 Faezeh Pousaneh  wrote:


Hi,

I have a system containing of a virtual site of carbon connected
symmetrically to two dummy massive sites (no charge). like :

M---C---M

My problem is the results I get from simulation of this system is not

equal

with results of single Carbon system simulation with mass of 2M (at

exactly

similar conditions)?
They produce different LJ coul energies, I have even tried for

non-charged

systems.

Thank you in advance for help,
Best regards
--
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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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] virtual site connected to dummy massive site

[Faezeh Pousaneh]

Hi Mark, sorry I am not convinced yet. I hope you did not misunderstand my
question, I have no charges in systems on any atoms. So the extra DOF do
not effect on potential.


Best regards


On Fri, Nov 24, 2017 at 11:03 AM, Mark Abraham 
wrote:

> Hi,
>
> Potential energy is a function of configuration. You can expect the same LJ
> energy if you compare the same configuration, ie that the distribution of
> states is identical. But if you would have the same total energy and a
> different distribution between PE and KE (because the DOF change) then you
> will not sample the same states.
>
> Mark
>
> On Fri, Nov 24, 2017 at 10:56 AM Faezeh Pousaneh 
> wrote:
>
> > Dear Mark,
> > thanks, but degrees of freedom goes to kinetic energies, still LJ
> energies
> > must be the same, yes?
> >
> >
> > Best regards
> >
> >
> > On Fri, Nov 24, 2017 at 8:22 AM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > Your systems have different available degrees of freedom, so they
> sample
> > > difference spaces. The energies you observe reflect that difference.
> > >
> > > Mark
> > >
> > > On Mon, 20 Nov 2017 18:18 Faezeh Pousaneh  wrote:
> > >
> > > > Hi,
> > > >
> > > > I have a system containing of a virtual site of carbon connected
> > > > symmetrically to two dummy massive sites (no charge). like :
> M---C---M
> > > > My problem is the results I get from simulation of this system is not
> > > equal
> > > > with results of single Carbon system simulation with mass of 2M (at
> > > exactly
> > > > similar conditions)?
> > > > They produce different LJ coul energies, I have even tried for
> > > non-charged
> > > > systems.
> > > >
> > > > Thank you in advance for help,
> > > > Best regards
> > > > --
> > > > 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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> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
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> > > >
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Re: [gmx-users] virtual site connected to dummy massive site

[Mark Abraham]

Hi,

Potential energy is a function of configuration. You can expect the same LJ
energy if you compare the same configuration, ie that the distribution of
states is identical. But if you would have the same total energy and a
different distribution between PE and KE (because the DOF change) then you
will not sample the same states.

Mark

On Fri, Nov 24, 2017 at 10:56 AM Faezeh Pousaneh 
wrote:

> Dear Mark,
> thanks, but degrees of freedom goes to kinetic energies, still LJ energies
> must be the same, yes?
>
>
> Best regards
>
>
> On Fri, Nov 24, 2017 at 8:22 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Your systems have different available degrees of freedom, so they sample
> > difference spaces. The energies you observe reflect that difference.
> >
> > Mark
> >
> > On Mon, 20 Nov 2017 18:18 Faezeh Pousaneh  wrote:
> >
> > > Hi,
> > >
> > > I have a system containing of a virtual site of carbon connected
> > > symmetrically to two dummy massive sites (no charge). like :  M---C---M
> > > My problem is the results I get from simulation of this system is not
> > equal
> > > with results of single Carbon system simulation with mass of 2M (at
> > exactly
> > > similar conditions)?
> > > They produce different LJ coul energies, I have even tried for
> > non-charged
> > > systems.
> > >
> > > Thank you in advance for help,
> > > Best regards
> > > --
> > > 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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> > >
> > --
> > Gromacs Users mailing list
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Re: [gmx-users] virtual site connected to dummy massive site

[Faezeh Pousaneh]

Dear Mark,
thanks, but degrees of freedom goes to kinetic energies, still LJ energies
must be the same, yes?


Best regards


On Fri, Nov 24, 2017 at 8:22 AM, Mark Abraham 
wrote:

> Hi,
>
> Your systems have different available degrees of freedom, so they sample
> difference spaces. The energies you observe reflect that difference.
>
> Mark
>
> On Mon, 20 Nov 2017 18:18 Faezeh Pousaneh  wrote:
>
> > Hi,
> >
> > I have a system containing of a virtual site of carbon connected
> > symmetrically to two dummy massive sites (no charge). like :  M---C---M
> > My problem is the results I get from simulation of this system is not
> equal
> > with results of single Carbon system simulation with mass of 2M (at
> exactly
> > similar conditions)?
> > They produce different LJ coul energies, I have even tried for
> non-charged
> > systems.
> >
> > Thank you in advance for help,
> > Best regards
> > --
> > 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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Re: [gmx-users] virtual site connected to dummy massive site

[Mark Abraham]

Hi,

Your systems have different available degrees of freedom, so they sample
difference spaces. The energies you observe reflect that difference.

Mark

On Mon, 20 Nov 2017 18:18 Faezeh Pousaneh  wrote:

> Hi,
>
> I have a system containing of a virtual site of carbon connected
> symmetrically to two dummy massive sites (no charge). like :  M---C---M
> My problem is the results I get from simulation of this system is not equal
> with results of single Carbon system simulation with mass of 2M (at exactly
> similar conditions)?
> They produce different LJ coul energies, I have even tried for non-charged
> systems.
>
> Thank you in advance for help,
> Best regards
> --
> 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.
>
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[gmx-users] virtual site connected to dummy massive site

[Faezeh Pousaneh]

Hi,

I have a system containing of a virtual site of carbon connected
symmetrically to two dummy massive sites (no charge). like :  M---C---M
My problem is the results I get from simulation of this system is not equal
with results of single Carbon system simulation with mass of 2M (at exactly
similar conditions)?
They produce different LJ coul energies, I have even tried for non-charged
systems.

Thank you in advance for help,
Best regards
-- 
Gromacs Users mailing list

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