[gmx-users] Notes and warnings using grompp

[Justin Lemkul]

On 9/28/12 4:10 PM, Sonia Milena Aguilera Segura wrote:
> Hi,
>
> I´m getting the following notes when using grompp to generate the tpr file. My system is a protein in water. I already checked the topology file and the sum of my charges are -13. Should I ignore it? Why is it assuming that value?
>
> NOTE 1 [file OmpC.top, line 23461]:
>    System has non-zero total charge: -13.000002
>    Total charge should normally be an integer.
>

You need to add counterions.  Please consult basic tutorial material.

> The second note is the following.
>
> Largest charge group radii for Van der Waals: 0.250, 0.244 nm
> Largest charge group radii for Coulomb:       0.084, 0.084 nm
>
> NOTE 2 [file min0.0.mdp]:
>    The sum of the two largest charge group radii (0.494582) is larger than
>    rlist (1.000000) - rvdw (0.900000)
>

http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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