Re: [gmx-users] non-neutral system

[Groenhof, Gerrit]

Hi,

The negative Coulomb energy is due to the interaction of your positively 
charged Argon atoms with the background charge of +10. However, I nevertheless 
expect that the dynamics will be that of all atoms repelling, as the uniform 
background charge does not exert a force in your case. Also, you could correct 
the Coulomb energy by computing the interaction of each ion with its own 
background charge, but that would only change your offset I think.  This my 
guess is that PME is still what you want to use, rather than cut-off.


Gerrit


Hi Justin,

I have a system of 500 Argon fluid each given a charge +0.20 (vdW
cut-off=0.8 nm). So I expect the system to have total positive coulomb
potential (repulsion). Below are simualtion results of PME and cut-off:


PME coulomb results:

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
LJ (SR)-2217.86   0.3424.5444  -0.214063
(kJ/mol)
Coulomb (SR)   993.008   0.145.39276  -0.435068  (kJ/mol)
Coul. recip.   -11192.7   0.159.86392  -0.470106
(kJ/mol)
Potential  -12417.50.633.2669   -1.11921
(kJ/mol)
Kinetic En. 1224.39   0.4444.2301   -2.79584
(kJ/mol)
Total Energy  -11193.1   0.9454.8503   -3.91503
(kJ/mol)
Conserved En.  -176697101446.14   -5008.59  (kJ/mol)
Temperature   196.74  0.0717.10709  -0.449246  (K)




Cut-off coulomb results (0.8 nm):

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
LJ (SR)-2231.64   0.5824.27352.05241
(kJ/mol)
Coulomb (SR)  94520.24.7221.879   -9.05937  (kJ/mol)
Potential   92288.54.5217.531   -7.00686
(kJ/mol)
Kinetic En.1257.31   0.4345.3804   0.778738
(kJ/mol)
Total Energy  93545.94.1221.992   -6.22759  (kJ/mol)
Conserved En. 518736  481842.2 283452  (kJ/mol)
Temperature197.031  0.0697.29193   -0.125132  (K)













Best regards


On Mon, Nov 6, 2017 at 1:06 PM, Jo?o Henriques  wrote:

> Hi Johannes,
>
> I just meant that from a purely theoretical point of view, it needs to be
> neutral. This has to do with the convergence of the outer infinite series,
> as the paper Micholas linked clearly states. I sincerely hope I'm not
> botching this up, but this is the conclusion I've withdrawn from reading
> the literature. Now, if the software implementation contains some tricks to
> account for this, that I'm not familiar with and will therefore leave that
> discussion for someone else more acquainted with it.
>
> Cheers,
> J
>
>
>
> On Mon, Nov 6, 2017 at 12:03 PM, Hermann, Johannes <
> j.herm...@lrz.tu-muenchen.de> wrote:
>
> > Hey Joao,
> >
> > are you sure? I think PME will introduce a neutralizing background
> charge?
> >
> > All the best
> >
> > Johannes
> >
> >
> >
> > On 06.11.2017 11:57, Jo?o Henriques wrote:
> >
> >> ?Hi,
> >>
> >> You shouldn't use PME without neutralizing the system's charge. ?It's a
> >> limitation of the Ewald summation. Take a look at the literature for
> >> further details.
> >>
> >> I don't know much about viscosity, so I'll leave that for someone else.
> >>
> >> Cheers,
> >> J
> >>
> >> On Mon, Nov 6, 2017 at 11:50 AM, Faezeh Pousaneh 
> >> wrote:
> >>
> >> Hi,
> >>>
> >>> I  have a system containing similar charged atoms. So the total charge
> is
> >>> not zero.
> >>>
> >>> Simulation results with cut-off coulomb seems reasonable,  but using
> PME
> >>> they are wrong (total columb potential is negative value which must be
> >>> positive). Any idea why?
> >>>
> >>> If I use counter-ions to neutralize the system, I am afraid the
> >>> properties
> >>> I am looking for (viscosity) will be influenced.
> >>>
> >>> 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.
> >>>
> >>>
> > --
> > __
> > *Technische Universit?t M?nchen*
> > *Johannes Hermann, M.Sc.*
> > Lehrstuhl f?r Bioverfahrenstechnik
> > Boltzmannstr. 15
> > D-85748 Garching
> > Tel: +49 8928915730
> > Fax: +49 8928915714
> >
> > Email: j.herm...@lrz.tum.de
> > http://www.biovt.mw.tum.de/
> >
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/Support
> > /Mailing_Lists/GMX-Users_List before 

Re: [gmx-users] non-neutral system

[Faezeh Pousaneh]

Hi Justin,

I have a system of 500 Argon fluid each given a charge +0.20 (vdW
cut-off=0.8 nm). So I expect the system to have total positive coulomb
potential (repulsion). Below are simualtion results of PME and cut-off:


PME coulomb results:

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
LJ (SR)-2217.86   0.3424.5444  -0.214063
(kJ/mol)
Coulomb (SR)   993.008   0.145.39276  -0.435068  (kJ/mol)
Coul. recip.   -11192.7   0.159.86392  -0.470106
(kJ/mol)
Potential  -12417.50.633.2669   -1.11921
(kJ/mol)
Kinetic En. 1224.39   0.4444.2301   -2.79584
(kJ/mol)
Total Energy  -11193.1   0.9454.8503   -3.91503
(kJ/mol)
Conserved En.  -176697101446.14   -5008.59  (kJ/mol)
Temperature   196.74  0.0717.10709  -0.449246  (K)




Cut-off coulomb results (0.8 nm):

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
LJ (SR)-2231.64   0.5824.27352.05241
(kJ/mol)
Coulomb (SR)  94520.24.7221.879   -9.05937  (kJ/mol)
Potential   92288.54.5217.531   -7.00686
(kJ/mol)
Kinetic En.1257.31   0.4345.3804   0.778738
(kJ/mol)
Total Energy  93545.94.1221.992   -6.22759  (kJ/mol)
Conserved En. 518736  481842.2 283452  (kJ/mol)
Temperature197.031  0.0697.29193   -0.125132  (K)













Best regards


On Mon, Nov 6, 2017 at 1:06 PM, João Henriques  wrote:

> Hi Johannes,
>
> I just meant that from a purely theoretical point of view, it needs to be
> neutral. This has to do with the convergence of the outer infinite series,
> as the paper Micholas linked clearly states. I sincerely hope I'm not
> botching this up, but this is the conclusion I've withdrawn from reading
> the literature. Now, if the software implementation contains some tricks to
> account for this, that I'm not familiar with and will therefore leave that
> discussion for someone else more acquainted with it.
>
> Cheers,
> J
>
>
>
> On Mon, Nov 6, 2017 at 12:03 PM, Hermann, Johannes <
> j.herm...@lrz.tu-muenchen.de> wrote:
>
> > Hey Joao,
> >
> > are you sure? I think PME will introduce a neutralizing background
> charge?
> >
> > All the best
> >
> > Johannes
> >
> >
> >
> > On 06.11.2017 11:57, João Henriques wrote:
> >
> >> ​Hi,
> >>
> >> You shouldn't use PME without neutralizing the system's charge. ​It's a
> >> limitation of the Ewald summation. Take a look at the literature for
> >> further details.
> >>
> >> I don't know much about viscosity, so I'll leave that for someone else.
> >>
> >> Cheers,
> >> J
> >>
> >> On Mon, Nov 6, 2017 at 11:50 AM, Faezeh Pousaneh 
> >> wrote:
> >>
> >> Hi,
> >>>
> >>> I  have a system containing similar charged atoms. So the total charge
> is
> >>> not zero.
> >>>
> >>> Simulation results with cut-off coulomb seems reasonable,  but using
> PME
> >>> they are wrong (total columb potential is negative value which must be
> >>> positive). Any idea why?
> >>>
> >>> If I use counter-ions to neutralize the system, I am afraid the
> >>> properties
> >>> I am looking for (viscosity) will be influenced.
> >>>
> >>> 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.
> >>>
> >>>
> > --
> > __
> > *Technische Universität München*
> > *Johannes Hermann, M.Sc.*
> > Lehrstuhl für Bioverfahrenstechnik
> > Boltzmannstr. 15
> > D-85748 Garching
> > Tel: +49 8928915730
> > Fax: +49 8928915714
> >
> > Email: j.herm...@lrz.tum.de
> > http://www.biovt.mw.tum.de/
> >
> >
> > --
> > 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] non-neutral system

[João Henriques]

Understood. Thank you Justin.

J

On Mon, Nov 6, 2017 at 1:11 PM, Justin Lemkul  wrote:

>
>
> On 11/6/17 7:06 AM, João Henriques wrote:
>
>> Hi Johannes,
>>
>> I just meant that from a purely theoretical point of view, it needs to be
>> neutral. This has to do with the convergence of the outer infinite series,
>> as the paper Micholas linked clearly states. I sincerely hope I'm not
>> botching this up, but this is the conclusion I've withdrawn from reading
>> the literature. Now, if the software implementation contains some tricks
>> to
>> account for this, that I'm not familiar with and will therefore leave that
>> discussion for someone else more acquainted with it.
>>
>
> For your reference, it's explained in dx.doi.org/10.1021/ct400626b
>
> All MD codes can do this when using PME, so it's not really a trick, just
> part of PME. It's not intuitive to most users, and not appropriate in many
> cases, hence the standard advice of "add counterions."
>
> -Justin
>
> --
> ==
>
> 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
>
> ==
>
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/Support
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>
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Re: [gmx-users] non-neutral system

[Justin Lemkul]

On 11/6/17 7:06 AM, João Henriques wrote:

Hi Johannes,

I just meant that from a purely theoretical point of view, it needs to be
neutral. This has to do with the convergence of the outer infinite series,
as the paper Micholas linked clearly states. I sincerely hope I'm not
botching this up, but this is the conclusion I've withdrawn from reading
the literature. Now, if the software implementation contains some tricks to
account for this, that I'm not familiar with and will therefore leave that
discussion for someone else more acquainted with it.


For your reference, it's explained in dx.doi.org/10.1021/ct400626b

All MD codes can do this when using PME, so it's not really a trick, 
just part of PME. It's not intuitive to most users, and not appropriate 
in many cases, hence the standard advice of "add counterions."


-Justin

--
==

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] non-neutral system

[João Henriques]

Hi Johannes,

I just meant that from a purely theoretical point of view, it needs to be
neutral. This has to do with the convergence of the outer infinite series,
as the paper Micholas linked clearly states. I sincerely hope I'm not
botching this up, but this is the conclusion I've withdrawn from reading
the literature. Now, if the software implementation contains some tricks to
account for this, that I'm not familiar with and will therefore leave that
discussion for someone else more acquainted with it.

Cheers,
J



On Mon, Nov 6, 2017 at 12:03 PM, Hermann, Johannes <
j.herm...@lrz.tu-muenchen.de> wrote:

> Hey Joao,
>
> are you sure? I think PME will introduce a neutralizing background charge?
>
> All the best
>
> Johannes
>
>
>
> On 06.11.2017 11:57, João Henriques wrote:
>
>> ​Hi,
>>
>> You shouldn't use PME without neutralizing the system's charge. ​It's a
>> limitation of the Ewald summation. Take a look at the literature for
>> further details.
>>
>> I don't know much about viscosity, so I'll leave that for someone else.
>>
>> Cheers,
>> J
>>
>> On Mon, Nov 6, 2017 at 11:50 AM, Faezeh Pousaneh 
>> wrote:
>>
>> Hi,
>>>
>>> I  have a system containing similar charged atoms. So the total charge is
>>> not zero.
>>>
>>> Simulation results with cut-off coulomb seems reasonable,  but using PME
>>> they are wrong (total columb potential is negative value which must be
>>> positive). Any idea why?
>>>
>>> If I use counter-ions to neutralize the system, I am afraid the
>>> properties
>>> I am looking for (viscosity) will be influenced.
>>>
>>> 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.
>>>
>>>
> --
> __
> *Technische Universität München*
> *Johannes Hermann, M.Sc.*
> Lehrstuhl für Bioverfahrenstechnik
> Boltzmannstr. 15
> D-85748 Garching
> Tel: +49 8928915730
> Fax: +49 8928915714
>
> Email: j.herm...@lrz.tum.de
> http://www.biovt.mw.tum.de/
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
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>
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>
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Re: [gmx-users] non-neutral system

[Hermann, Johannes]

In the link it says:

"Note for PME 
 
users: It is possible to use a uniform neutralizing background charge in 
PME 
 
to compensate for a system with a net background charge. There is 
probably nothing wrong with this in principle, because the uniform 
charge will not perturb the dynamics. Nevertheless, it is standard 
practice to actually add counter-ions 
 to make 
the system net neutral."


Hence, it is also possible without adding - right?


On 06.11.2017 12:45, Faezeh Pousaneh wrote:

Thank you guys.

Johanns, I think one must add counter-ions by himself (which I do not
want), as written here
http://www.gromacs.org/Documentation/Errors#System_has_non-zero_total_charge





Best regards


On Mon, Nov 6, 2017 at 12:03 PM, Hermann, Johannes <
j.herm...@lrz.tu-muenchen.de> wrote:


Hey Joao,

are you sure? I think PME will introduce a neutralizing background charge?

All the best

Johannes



On 06.11.2017 11:57, João Henriques wrote:


​Hi,

You shouldn't use PME without neutralizing the system's charge. ​It's a
limitation of the Ewald summation. Take a look at the literature for
further details.

I don't know much about viscosity, so I'll leave that for someone else.

Cheers,
J

On Mon, Nov 6, 2017 at 11:50 AM, Faezeh Pousaneh 
wrote:

Hi,

I  have a system containing similar charged atoms. So the total charge is
not zero.

Simulation results with cut-off coulomb seems reasonable,  but using PME
they are wrong (total columb potential is negative value which must be
positive). Any idea why?

If I use counter-ions to neutralize the system, I am afraid the
properties
I am looking for (viscosity) will be influenced.

Best regards
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--
__
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.herm...@lrz.tum.de
http://www.biovt.mw.tum.de/


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--
__
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.herm...@lrz.tum.de
http://www.biovt.mw.tum.de/

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Re: [gmx-users] non-neutral system

[Justin Lemkul]

On 11/6/17 5:50 AM, Faezeh Pousaneh wrote:

Hi,

I  have a system containing similar charged atoms. So the total charge is
not zero.

Simulation results with cut-off coulomb seems reasonable,  but using PME
they are wrong (total columb potential is negative value which must be
positive). Any idea why?


Cutoff electrostatics are a poor method to use. State of the art decades 
ago, but PME is the de facto standard. Why should the total 
electrostatic energy be positive in your case? What exactly is your system?



If I use counter-ions to neutralize the system, I am afraid the properties


You may not necessarily need counterions, but you'll have to explain 
more about what your system is (see my other post regarding the 
neutralizing background plasma).


-Justin


I am looking for (viscosity) will be influenced.

Best regards


--
==

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] non-neutral system

[Justin Lemkul]

On 11/6/17 6:03 AM, Hermann, Johannes wrote:

Hey Joao,

are you sure? I think PME will introduce a neutralizing background 
charge?




It does. Whether or not it's appropriate is another matter. For 
homogeneous systems, it's fine, but if dealing with something 
heterogeneous like a membrane, there are serious artifacts in this approach.


-Justin


All the best

Johannes


On 06.11.2017 11:57, João Henriques wrote:

​Hi,

You shouldn't use PME without neutralizing the system's charge. ​It's a
limitation of the Ewald summation. Take a look at the literature for
further details.

I don't know much about viscosity, so I'll leave that for someone else.

Cheers,
J

On Mon, Nov 6, 2017 at 11:50 AM, Faezeh Pousaneh 
wrote:


Hi,

I  have a system containing similar charged atoms. So the total 
charge is

not zero.

Simulation results with cut-off coulomb seems reasonable,  but using 
PME

they are wrong (total columb potential is negative value which must be
positive). Any idea why?

If I use counter-ions to neutralize the system, I am afraid the 
properties

I am looking for (viscosity) will be influenced.

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] non-neutral system

[Faezeh Pousaneh]

Thank you guys.

Johanns, I think one must add counter-ions by himself (which I do not
want), as written here
http://www.gromacs.org/Documentation/Errors#System_has_non-zero_total_charge





Best regards


On Mon, Nov 6, 2017 at 12:03 PM, Hermann, Johannes <
j.herm...@lrz.tu-muenchen.de> wrote:

> Hey Joao,
>
> are you sure? I think PME will introduce a neutralizing background charge?
>
> All the best
>
> Johannes
>
>
>
> On 06.11.2017 11:57, João Henriques wrote:
>
>> ​Hi,
>>
>> You shouldn't use PME without neutralizing the system's charge. ​It's a
>> limitation of the Ewald summation. Take a look at the literature for
>> further details.
>>
>> I don't know much about viscosity, so I'll leave that for someone else.
>>
>> Cheers,
>> J
>>
>> On Mon, Nov 6, 2017 at 11:50 AM, Faezeh Pousaneh 
>> wrote:
>>
>> Hi,
>>>
>>> I  have a system containing similar charged atoms. So the total charge is
>>> not zero.
>>>
>>> Simulation results with cut-off coulomb seems reasonable,  but using PME
>>> they are wrong (total columb potential is negative value which must be
>>> positive). Any idea why?
>>>
>>> If I use counter-ions to neutralize the system, I am afraid the
>>> properties
>>> I am looking for (viscosity) will be influenced.
>>>
>>> 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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>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> __
> *Technische Universität München*
> *Johannes Hermann, M.Sc.*
> Lehrstuhl für Bioverfahrenstechnik
> Boltzmannstr. 15
> D-85748 Garching
> Tel: +49 8928915730
> Fax: +49 8928915714
>
> Email: j.herm...@lrz.tum.de
> http://www.biovt.mw.tum.de/
>
>
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Re: [gmx-users] non-neutral system

[Hermann, Johannes]

Hey Joao,

are you sure? I think PME will introduce a neutralizing background charge?

All the best

Johannes


On 06.11.2017 11:57, João Henriques wrote:

​Hi,

You shouldn't use PME without neutralizing the system's charge. ​It's a
limitation of the Ewald summation. Take a look at the literature for
further details.

I don't know much about viscosity, so I'll leave that for someone else.

Cheers,
J

On Mon, Nov 6, 2017 at 11:50 AM, Faezeh Pousaneh 
wrote:


Hi,

I  have a system containing similar charged atoms. So the total charge is
not zero.

Simulation results with cut-off coulomb seems reasonable,  but using PME
they are wrong (total columb potential is negative value which must be
positive). Any idea why?

If I use counter-ions to neutralize the system, I am afraid the properties
I am looking for (viscosity) will be influenced.

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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send a mail to gmx-users-requ...@gromacs.org.



--
__
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.herm...@lrz.tum.de
http://www.biovt.mw.tum.de/

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Re: [gmx-users] non-neutral system

[Smith, Micholas D.]

A requirement of PME is that the net charge is zero. Adding counter-ions would 
be considered standard-fare. Check out the paper:  
https://www.unc.edu/~perera/PAPERS/JChemPhys_1995_103_8577.pdf for details (A 
smooth particle mesh Ewald method).

Best of luck

===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Faezeh 
Pousaneh <fpoosa...@gmail.com>
Sent: Monday, November 06, 2017 5:50 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] non-neutral system

Hi,

I  have a system containing similar charged atoms. So the total charge is
not zero.

Simulation results with cut-off coulomb seems reasonable,  but using PME
they are wrong (total columb potential is negative value which must be
positive). Any idea why?

If I use counter-ions to neutralize the system, I am afraid the properties
I am looking for (viscosity) will be influenced.

Best regards
--
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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] non-neutral system

[João Henriques]

​Hi,

You shouldn't use PME without neutralizing the system's charge. ​It's a
limitation of the Ewald summation. Take a look at the literature for
further details.

I don't know much about viscosity, so I'll leave that for someone else.

Cheers,
J

On Mon, Nov 6, 2017 at 11:50 AM, Faezeh Pousaneh 
wrote:

> Hi,
>
> I  have a system containing similar charged atoms. So the total charge is
> not zero.
>
> Simulation results with cut-off coulomb seems reasonable,  but using PME
> they are wrong (total columb potential is negative value which must be
> positive). Any idea why?
>
> If I use counter-ions to neutralize the system, I am afraid the properties
> I am looking for (viscosity) will be influenced.
>
> 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
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[gmx-users] non-neutral system

[Faezeh Pousaneh]

Hi,

I  have a system containing similar charged atoms. So the total charge is
not zero.

Simulation results with cut-off coulomb seems reasonable,  but using PME
they are wrong (total columb potential is negative value which must be
positive). Any idea why?

If I use counter-ions to neutralize the system, I am afraid the properties
I am looking for (viscosity) will be influenced.

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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Re: [gmx-users] Non-neutral system with iron-sulfur clusters

[Justin Lemkul]

On 6/14/16 7:37 AM, Marlon Sidore wrote:

I checked everything and even by adding the numbers on the paper and the
cystein charges from amber03 (the FF they used in the paper) the resulting
charge isn't an integer.

The paper has charges for the Fe (4x), the S (4x) from the cluster, the S
from the CYS bound to it and the CB bound to the previous S in CYS. Simply
adding them and the other atoms from CYS (4x in case of the CYS atoms)
doesn't yield an integer. I didn't count S and CB twice either.

The resulting charge from the whole 4CYS-4Fe-4S is -1.233684.



You should contact the corresponding author of the paper.  This is not a GROMACS 
problem.


-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] Non-neutral system with iron-sulfur clusters

[Marlon Sidore]

I checked everything and even by adding the numbers on the paper and the
cystein charges from amber03 (the FF they used in the paper) the resulting
charge isn't an integer.

The paper has charges for the Fe (4x), the S (4x) from the cluster, the S
from the CYS bound to it and the CB bound to the previous S in CYS. Simply
adding them and the other atoms from CYS (4x in case of the CYS atoms)
doesn't yield an integer. I didn't count S and CB twice either.

The resulting charge from the whole 4CYS-4Fe-4S is -1.233684.

Marlon Sidore


PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France


2016-06-14 13:20 GMT+02:00 Justin Lemkul :

>
>
> On 6/14/16 4:59 AM, Marlon Sidore wrote:
>
>> Hello everyone,
>>
>> On my quest to use the parameters for iron-sulfur clusters from [1] I
>> realized that the resulting clusters are not neutral. Indeed, even though
>> the charges of the 2 CYS atom (SG and CB) are modified, the overall charge
>> of the cluster + the 4 CYS isn't a round number.
>>
>> Should I worry ?
>>
>>
> Non-integer charges are totally non-physical, so using such a topology
> would be wrong.  Check carefully that you've assigned everything correctly.
>
> -Justin
>
> 1. Smith, D. M. A., Xiong, Y., Straatsma, T. P., Rosso, K. M. & Squier, T.
>> C. Force-Field Development and Molecular Dynamics of [NiFe] Hydrogenase.
>> J.
>> Chem. Theory Comput. 8, 2103–2114 (2012).
>>
>> Marlon Sidore
>>
>>
>> PhD Student
>> Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
>> CNRS - UMR7255
>> 31, Chemin Joseph Aiguier
>> 13402 cedex 20 Marseille
>> France
>>
>>
> --
> ==
>
> 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
>
> ==
> --
> 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] Non-neutral system with iron-sulfur clusters

[Justin Lemkul]

On 6/14/16 4:59 AM, Marlon Sidore wrote:

Hello everyone,

On my quest to use the parameters for iron-sulfur clusters from [1] I
realized that the resulting clusters are not neutral. Indeed, even though
the charges of the 2 CYS atom (SG and CB) are modified, the overall charge
of the cluster + the 4 CYS isn't a round number.

Should I worry ?



Non-integer charges are totally non-physical, so using such a topology would be 
wrong.  Check carefully that you've assigned everything correctly.


-Justin


1. Smith, D. M. A., Xiong, Y., Straatsma, T. P., Rosso, K. M. & Squier, T.
C. Force-Field Development and Molecular Dynamics of [NiFe] Hydrogenase. J.
Chem. Theory Comput. 8, 2103–2114 (2012).

Marlon Sidore


PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France



--
==

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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[gmx-users] Non-neutral system with iron-sulfur clusters

[Marlon Sidore]

Hello everyone,

On my quest to use the parameters for iron-sulfur clusters from [1] I
realized that the resulting clusters are not neutral. Indeed, even though
the charges of the 2 CYS atom (SG and CB) are modified, the overall charge
of the cluster + the 4 CYS isn't a round number.

Should I worry ?

1. Smith, D. M. A., Xiong, Y., Straatsma, T. P., Rosso, K. M. & Squier, T.
C. Force-Field Development and Molecular Dynamics of [NiFe] Hydrogenase. J.
Chem. Theory Comput. 8, 2103–2114 (2012).

Marlon Sidore


PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France
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[gmx-users] Non-neutral system

[Ali Alizadeh]

Dear All users,

I want to simulate a non-neutral system including cations with gromacs. It
can be possible?

I want to use Ewald summation for long for calculating range range
interactions.

I see in Error page of gromacs:

Note for PME users: It is possible to use a uniform neutralizing
background charge in PME to compensate for a system with a net
background charge. There is probably nothing wrong with this in
principle, because the uniform charge will not perturb the dynamics.



It means I can not use Ewlad for charged systems?

Besides, I can not realize that how neutralization can be done by
uniform neutralizing background charge. Which part of gromacs do it?


-- 
Sincerely

Ali Alizadeh
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Re: [gmx-users] Non-neutral system

[Carsten Kutzner]

Hi,

technically, you can use PME with charged systems in Gromacs. However,
if the charges in your system are distributed inhomogeneously (as, e.g.
in a water/membrane system), you will get artefacts, as described in

http://www.mpibpc.mpg.de/14063977/Hub_2014_JCTC.pdf

Best,
  Carsten


On 23 Apr 2014, at 12:58, Ali Alizadeh ali.alizadehmoja...@gmail.com wrote:

 Dear All users,
 
 I want to simulate a non-neutral system including cations with gromacs. It
 can be possible?
 
 I want to use Ewald summation for long for calculating range range
 interactions.
 
 I see in Error page of gromacs:
 
 Note for PME users: It is possible to use a uniform neutralizing
 background charge in PME to compensate for a system with a net
 background charge. There is probably nothing wrong with this in
 principle, because the uniform charge will not perturb the dynamics.
 
 
 
 It means I can not use Ewlad for charged systems?
 
 Besides, I can not realize that how neutralization can be done by
 uniform neutralizing background charge. Which part of gromacs do it?
 
 
 -- 
 Sincerely
 
 Ali Alizadeh
 -- 
 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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Re: [gmx-users] Non-neutral system

[Ali Alizadeh]

Dear Carsten,
Thank you very much for your reply.
Yes, it is distributed inhomogeneously. In fact I want to investigate the
solvation energy of cations in water(12 cations, total charge +24e).
Initial configuration includes cations near the surface of water and then
they should diffuse into the water bulk.
Besides, I am reproducing the results of an article(NVT ensemble, Nose
hoover), so I want to use Ewald for making sure that all options are
similar. You meant it can be possible with Ewald?

--

Hi,

technically, you can use PME with charged systems in Gromacs. However,
if the charges in your system are distributed inhomogeneously (as, e.g.
in a water/membrane system), you will get artefacts, as described in
http://www.mpibpc.mpg.de/14063977/Hub_2014_JCTC.pdf

Best,
  Carsten


On 23 Apr 2014, at 12:58, Ali Alizadeh ali.alizadehmojarad at
gmail.com https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
wrote:

* Dear All users,
* * I want to simulate a non-neutral system including cations with gromacs. It
** can be possible?
* * I want to use Ewald summation for long for calculating range range
** interactions.
* * I see in Error page of gromacs:
* * Note for PME users: It is possible to use a uniform neutralizing
** background charge in PME to compensate for a system with a net
** background charge. There is probably nothing wrong with this in
** principle, because the uniform charge will not perturb the dynamics.
* * 
* * It means I can not use Ewlad for charged systems?
* * Besides, I can not realize that how neutralization can be done by
** uniform neutralizing background charge. Which part of gromacs do it?
*  * --
** Sincerely
* * Ali Alizadeh*


-- 
Sincerely

Ali Alizadeh
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