<div style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial"><div style="margin: 0;">Hi Developers,</div><div style="margin: 0;"><br></div><div style="margin: 0;">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.</div><div style="margin: 0;">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+, <br></div><div style="margin: 0;">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.</div><div style="margin: 0;"><br></div><div style="margin: 0;">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.</div><div style="margin: 0;"><br></div><div style="margin: 0;">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+,</div><div style="margin: 0;">The integration is bigger (1.5-2 times) than the output from -cn. <br></div><div style="margin: 0;"><br></div><div style="margin: 0;">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.</div><div style="margin: 0;"><br></div><div style="margin: 0;">So, I wonder whether other users encountered a similar problem. Or could developers help me understand what happens?</div><div style="margin: 0;"><br></div><div style="margin: 0;">Thanks in advance</div><div style="margin: 0;">Best</div><div style="margin: 0;"><br></div><div style="margin: 0;">iSimuly<br></div><div style="margin: 0;"><br></div></div><br><br><span title="neteasefooter"><p> </p></span>