[gmx-users] Broken molecule across periodic boundary: "The sum of the two largest charge group radii (xxx) is larger than rlist (xxx)"

[yunshi11 .]

Hi there,

I understand this is an old issue, but no one seems to have a solution?

So I want to take a snapshot from the middle of a MD trajectory (like 67ns
point from a 100ns trajectory) to start a new MD under different
temperature, preferably with all solvent molecules (waters and ions).
However, after using trjconv -pbc to make molecules "whole" or "nojump", I
am still having the same warning:

......
Number of degrees of freedom in T-Coupling group Water_and_ions is 314583.28
Largest charge group radii for Van der Waals: 11.794, 9.979 nm
Largest charge group radii for Coulomb:       11.794, 11.748 nm

WARNING 1 [file nvt.mdp]:
  The sum of the two largest charge group radii (23.542278) is larger than
  rlist (1.000000)


Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 112x112x112, spacing 0.120 0.120 0.120
Estimate for the relative computational load of the PME mesh part: 0.27
This run will generate roughly 42 Mb of data

There was 1 warning

-------------------------------------------------------
Program grompp, VERSION 4.6.5
Source code file:
/global/software/src/gromacs/gromacs-4.6.5/src/kernel/grompp.c, line: 1910

Fatal error:
Too many warnings (1), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


I have also tried removing solvents (partially and completely), and found
that I could only resolve this issue after removing all of the solvents
(waters and ions).

Regards,
Yun


On Wed, Jun 11, 2014 at 11:07 AM, yunshi11 . <yunshi09 at gmail.com> wrote:

> Hi there,
>
> I understand this is an old issue, but no one seems to have a solution?
>
> So I want to take a snapshot from the middle of a MD trajectory (like 67ns
> point from a 100ns trajectory), preferably with all solvent molecules
> (waters and ions). However, after using trjconv -pbc to make molecules
> "whole" or "nojump", I am still having the same warning:
>
> ......
> Number of degrees of freedom in T-Coupling group Water_and_ions is
> 314583.28
> Largest charge group radii for Van der Waals: 11.794, 9.979 nm
> Largest charge group radii for Coulomb:       11.794, 11.748 nm
>
> WARNING 1 [file nvt.mdp]:
>   The sum of the two largest charge group radii (23.542278) is larger than
>   rlist (1.000000)
>
>
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 112x112x112, spacing 0.120 0.120 0.120
> Estimate for the relative computational load of the PME mesh part: 0.27
> This run will generate roughly 42 Mb of data
>
> There was 1 warning
>
> -------------------------------------------------------
> Program grompp, VERSION 4.6.5
> Source code file:
> /global/software/src/gromacs/gromacs-4.6.5/src/kernel/grompp.c, line: 1910
>
> Fatal error:
> Too many warnings (1), grompp terminated.
> If you are sure all warnings are harmless, use the -maxwarn option.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> I have also tried removing solvents (partially and completely), and found
> that I could only resolve this issue after removing all of the solvents
> (waters and ions).
>
> Regards,
> Yun
>