[gmx-users] How to deal with "non-zero total charge" problem in gromacs?

[Dallas Warren]

Well there's your problem!  Don't ignore things like this, the software is
giving you the warning for a reason.

You are going to have to go through that process again, and fix the
starting coordinate file you are using, or the processing, depending on
which atoms are the ones missing. The residue database of the forcefield
being used to generate the topology expects each residue to have particular
atoms and atom names for each residue. If some of those are missing, then
you need to address that fact.

http://manual.gromacs.org/documentation/current/user-guide/run-time-errors.html#warning-atom-x-is-missing-in-residue-xxx-y-in-the-pdb-file

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Fri, 2 Aug 2019 at 11:45, sunyeping <sunyeping at aliyun.com> wrote:

> I don't know where the non-integral charges come from. But When preparing
> the gro file from the initial PDB file (a protein-DNA complex), I got a
> information saying that there are 24 atoms missing in the structure, but I
> can't tell what are these atoms. Could you tell me how to fix the atom
> missing problem? Thank you.
> ------------------------------------------------------------------
> From:孙业平 <sunyeping at aliyun.com>
> Sent At:2019 Aug. 1 (Thu.) 13:18
> To:gromacs.org_gmx-users <gromacs.org_gmx-users at maillist.sys.kth.se>;
> Bratin Kumar Das <177cy500.bratin at nitk.edu.in>
> Subject:Re: [gmx-users] How to deal with "non-zero total charge" problem
> in gromacs?
>
>
>
> ------------------------------------------------------------------
> From:Bratin Kumar Das <177cy500.bratin at nitk.edu.in>
> Sent At:2019 Aug. 1 (Thu.) 12:31
> To:gromacs <gmx-users at gromacs.org>; 孙业平 <sunyeping at aliyun.com>
> Subject:Re: [gmx-users] How to deal with "non-zero total charge" problem
> in gromacs?
>
> Hi,
>     Yes you can use the (-maxwarn) flag to overcome the error. But better
> to optimize the starting structure to reduce the excess charge of your
> system.
>
> Thank you for the replay. But I have no idea of how to optimize the
> starting structure to reduce the excess charge. Could you give me some
> hints or examples or something?
>
> Best regards
>
>
>
> On Thu, Aug 1, 2019 at 9:35 AM sunyeping <sunyeping at aliyun.com> wrote:
> Dear all,
>
>  I am trying to do MD simulation with protein-DNA complex with gromacs.
> When using gmx grompp to generate the tpr file for energy minimization, I
> enconters a fatal error:
>
>  Fatal error:
>  Too many warnings (1).
>  If you are sure all warnings are harmless, use the -maxwarn option.
>
>  There are two notes and one warning arose with grompp, and they are:
>
>  NOTE 1 [file em.mdp]:
>    With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>    that with the Verlet scheme, nstlist has no effect on the accuracy of
>    your simulation.
>  NOTE 2 [file topol.top, line 55]:
>    System has non-zero total charge: -0.189598
>    Total charge should normally be an integer. See
> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>    for discussion on how close it should be to an integer.
>  WARNING 1 [file topol.top, line 55]:
>    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.
>
>  It seems that the -0.189598 non-zero charge causes the fatal error. Is it
> possible to correct it? and how? or could I use the -maxwarn option as
> mentioned in the error message?
>
>  Best regards
>  --
>  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.
> --
> 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.
> --
> 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.