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

[SAKO MIRZAIE]

Dear Mark,

Thank you for your suggestion. That was true. I solved the problem.
Best,

On Fri, Dec 6, 2019 at 3:39 AM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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/
>> --
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>

-- 
***********************************************
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/