[gmx-users] The total charge is not integer : -0.00465

[SAKO MIRZAIE]

Dear Justin,

Thank you for your answer. when I use just one chain of polymer with the
protein, the charge is an integer but when I employ "insert molecules" to
add more than one polymer chain, the charge will not be an integer. I am
wondering what's the problem?

Best regards

On Tue, Dec 3, 2019 at 4:04 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/3/19 3:59 PM, SAKO MIRZAIE wrote:
> > Hi All,
> > I did some MD  studies on a protein: polymer system. After running
> grompp,
> > it said, "the total charge is not an integer". the total charge is
> -0.00465.
> > Can I continue the MD by adding -maxwarn flag? or it will be a problem
> and
> > I will get unrealistic results?
>
> In general, it is never a good idea to use -maxwarn.
>
> The magnitude of that total charge is suspiciously high and you should
> check your topology for proper charge assignment.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
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>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>

-- 
***********************************************
Sako Mirzaie
Sako Mirzaie
Ph.D. in biochemistry, Assistant Professor, Science Faculty, Islamic Azad
University of Sanandaj, Sanandaj, Iran

Visiting Professor, Advanced Pharmaceutics

& Drug Delivery Laboratory

Leslie Dan Faculty of Pharmacy

University of Toronto

144 College Street, Toronto, Ontario

Canada M5S 3M2

http://scholar.google.com/citations?user=viwZvVAAAAAJ&hl=en

http://www.scopus.com/authid/detail.url?authorId=54886431500

http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie
https://www.researchgate.net/profile/Sako_Mirzaie/publications/