[gmx-developers] unexpected results from gmx rdf.

[isimuly]

Hi Developers,


I am confused by result got by gmx rdf command. There are charged monomers and counterions,K+, in my systems. I calculated the g(r) using the gmx rdf command.
I used the "  gmx rdf -f traj.trr -s npt.tpr -n index.ndx -b 10000  -bin 0.01  -o rdf_check.xvg  -cn rdf_cn.xvg  -selrpos atom -seltype atom" to calculate the g(r) of  K+/K+,

and used  "  gmx rdf -f traj.trr -s npt.tpr -n index.ndx -b 10000  -bin 0.01  -o rdf_check.xvg  -cn rdf_cn.xvg  -selrpos res_com -seltype res_com" to calculate the g(r) of monomer/monomer or monomer/K+ because I want to use the center of mass of charged monomers as the reference.


Then I integrate the g(r)*pho_local (it should be the  K+ number in the sphere with radius, rmax ) to obtain the cumulative number to compare with the output result from -cn.


When I used the g(r) for K+/K+ to test, the integration result is close to the output from -cn (I chose the value at rmax to compare). However, When I used the g(r) for monomer/monomer or monomer/K+,
The integration is bigger (1.5-2 times) than the output from -cn.



I think this might be caused by how to choose the reference, center of mass or atom (I used the same integration script I wrote). I try to find why this occurs. One is I misunderstand/misused the command, the other is there is a bug of gromacs code.


So, I wonder whether other users encountered a similar problem.   Or could developers help me understand what happens?


Thanks in advance
Best


iSimuly

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