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

[sunyeping]

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.