Re: [gmx-users] Charge system simulation problem

[Justin Lemkul]

On 11/26/18 11:02 PM, Karpurmanjari Kakati wrote:

Hi Justin,

Because I have self generated the itp file, and that's the only place where
charge in terms of partial charge is added. Is the problem lying there?


Yes. Your charges don't add up to an integer, so there is something 
wrong somewhere.



Also can't  we denote the partial charges in decimal because  in real some
atoms will have net charges that can be decimal values due to presence or
absence of electronegative atoms adjacent to it?


Yes, that's the typical approach for partial charge assignment.




And are all the other notes and warnings generated are all because of that?


No. Using PME with a system with net charge can have severe artifacts. 
PME includes a neutralizing background plasma, but that is often 
insufficiently accurate. The conventional approach is to add counterions 
to the solution to balance the net charge of the solute.


-Justin



karpurmanjari

On Mon, Nov 26, 2018 at 10:31 AM Karpurmanjari Kakati <
ch18resch01...@iith.ac.in> wrote:


Dear All,

My System contains, while doing NVT of the same, I got the following Note






*NOTE 1 [file sa.top, line 80]:  System has non-zero total charge:
12.936997  Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for
discussion on how close it should be to an integer.*


This is possibly because of  the partial charges in the molecules in the
ITP fie.
My doubt is can't I have a system with non zero and a decimal charge value.


Also I got the following warning:






*WARNING 1 [file sa.top, line 80]:  You are using Ewald electrostatics in
a system with net charge. This can  lead to severe artifacts, such as ions
moving into regions with low  dielectric, due to the uniform background
charge. We suggest to  neutralize your system with counter ions, possibly
in combination with a  physiological salt concentration.*

Can Someone help me with this?

Also this :







*Velocities were taken from a Maxwell distribution at 300 KRemoving all
charge groups because cutoff-scheme=VerletAnalysing residue names:There
are: 1  Other residuesThere are: 10  Water residues*


Removing all charge group because the cut off scheme is verlet.

If That happens then will it show the behavior I want to see. Or shall I
put any other scheme on that ?

Please help




--
==

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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.

Re: [gmx-users] Charge system simulation problem

[Karpurmanjari Kakati]

Hi Justin,

Because I have self generated the itp file, and that's the only place where
charge in terms of partial charge is added. Is the problem lying there?
Also can't  we denote the partial charges in decimal because  in real some
atoms will have net charges that can be decimal values due to presence or
absence of electronegative atoms adjacent to it?


And are all the other notes and warnings generated are all because of that?


karpurmanjari

On Mon, Nov 26, 2018 at 10:31 AM Karpurmanjari Kakati <
ch18resch01...@iith.ac.in> wrote:

> Dear All,
>
> My System contains, while doing NVT of the same, I got the following Note
>
>
>
>
>
>
> *NOTE 1 [file sa.top, line 80]:  System has non-zero total charge:
> 12.936997  Total charge should normally be an integer. See
> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>   for
> discussion on how close it should be to an integer.*
>
>
> This is possibly because of  the partial charges in the molecules in the
> ITP fie.
> My doubt is can't I have a system with non zero and a decimal charge value.
>
>
> Also I got the following warning:
>
>
>
>
>
>
> *WARNING 1 [file sa.top, line 80]:  You are using Ewald electrostatics in
> a system with net charge. This can  lead to severe artifacts, such as ions
> moving into regions with low  dielectric, due to the uniform background
> charge. We suggest to  neutralize your system with counter ions, possibly
> in combination with a  physiological salt concentration.*
>
> Can Someone help me with this?
>
> Also this :
>
>
>
>
>
>
>
> *Velocities were taken from a Maxwell distribution at 300 KRemoving all
> charge groups because cutoff-scheme=VerletAnalysing residue names:There
> are: 1  Other residuesThere are: 10  Water residues*
>
>
> Removing all charge group because the cut off scheme is verlet.
>
> If That happens then will it show the behavior I want to see. Or shall I
> put any other scheme on that ?
>
> Please help
>
>
-- 
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.

Re: [gmx-users] Charge system simulation problem

[Justin Lemkul]

On 11/26/18 12:01 AM, Karpurmanjari Kakati wrote:

Dear All,

My System contains, while doing NVT of the same, I got the following Note






*NOTE 1 [file sa.top, line 80]:  System has non-zero total charge:
12.936997  Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for
discussion on how close it should be to an integer.*


This is possibly because of  the partial charges in the molecules in the
ITP fie.


Something isn't parametrized correctly because you need to have an 
integer charge. Your total charge is not physical.


-Justin


My doubt is can't I have a system with non zero and a decimal charge value.


Also I got the following warning:






*WARNING 1 [file sa.top, line 80]:  You are using Ewald electrostatics in a
system with net charge. This can  lead to severe artifacts, such as ions
moving into regions with low  dielectric, due to the uniform background
charge. We suggest to  neutralize your system with counter ions, possibly
in combination with a  physiological salt concentration.*

Can Someone help me with this?

Also this :







*Velocities were taken from a Maxwell distribution at 300 KRemoving all
charge groups because cutoff-scheme=VerletAnalysing residue names:There
are: 1  Other residuesThere are: 10  Water residues*


Removing all charge group because the cut off scheme is verlet.

If That happens then will it show the behavior I want to see. Or shall I
put any other scheme on that ?

Please help


--
==

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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.