[gmx-users] DNA-protein complex distorted in vacuum simulation

[Erik Marklund]

On 25 Mar 2015, at 11:43, rahul dhakne <rahuldhakne89 at gmail.com<mailto:rahuldhakne89 at gmail.com>> wrote:

NOTE 1 [file topol.top, line 44]:
 System has non-zero total charge: -163.000000
 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.

As the system is highly negatively charged it would have caused the
structure to distort or it could be  an artifact of visualization software??

Hi Rahul,

Possibly both, but that kind of net charge is likely to cause it to deform in the gas phase where the effective dielectric constant is much lower than in solution.

Do you have mass-spectrometry data for the complex? If so, what is the charge?

Erik