[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 <
> ch18resch01002 at 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
>> <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 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

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

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