[gmx-users] Charge system simulation problem

[Karpurmanjari Kakati]

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
<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: 100000 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 Lemkul]

Post by Karpurmanjari Kakati
Dear All,
My System contains, while doing NVT of the same, I got the following Note
12.936997 Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
<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

Post by Karpurmanjari Kakati
My doubt is can't I have a system with non zero and a decimal charge value.
*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?
*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: 100000 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

***@vt.edu | [phone]
http://www.thelemkullab.com

==================================================

[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 <

Post by Karpurmanjari Kakati
Dear All,
My System contains, while doing NVT of the same, I got the following Note
12.936997 Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
<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.
*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?
*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: 100000 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 Lemkul]

Post by 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?

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

Post by Karpurmanjari Kakati
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.

Post by Karpurmanjari Kakati
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

Post by Karpurmanjari Kakati
karpurmanjari
On Mon, Nov 26, 2018 at 10:31 AM Karpurmanjari Kakati <

Post by Karpurmanjari Kakati
Dear All,
My System contains, while doing NVT of the same, I got the following Note
12.936997 Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
<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.
*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?
*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: 100000 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

***@vt.edu | [phone]
http://www.thelemkullab.com

==================================================