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

[Mark Abraham]

Hi,

If, for example, you inserted 465 polymer molecules each with charge -.001
then the most appropriate path forward is to make the total charge of each
molecule be neutral. But we don't know enough about what you're doing yet.

Mark

On Thu, 5 Dec 2019 at 23:34, SAKO MIRZAIE <sako.biochem at gmail.com> wrote:

> 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
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > 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/
> --
> 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-request at gromacs.org.
>