Hi,<br><br>I'm getting better to use Gromacs owing to many posts on this sites :) .<br><br>I have several questions about adding the counter-ions.<br><br>My system has a number of N2 molecules which has charge, -0.40484(for single N) X 2.<br>
Thus, I have to add some counter-ions to make the system neutral.<br><br>However, because I'm newbie on Gromacs, I thought of several clumsy ways myself. <br><br>#1. Add virtual sites (virtual atoms) which has counter-ions like below.<br>
<br>[ atomtypes ] <br>; name mass charge ptype sigma epsilon <br>DUM 0 0.80968 V 0.0 0.0<br><br>I set the coordinates of each virtual DUM atoms to the center of N2 molecules. <br><br>#2. using genion in Gromacs.<br>
<br>But, I have no idea on this. What molecules do I have to designate to charge plus ion using genion ?? <br><br>I typed below line.<br>genion -s md_0_1.tpr -n index.ndx -o ton_genion.pdb -g md_0_1_genion.log -p topol_genion.top -np 322 -pname dum -pq 0.80968 <br>
<br>and selected N2 molecules which is diffusing particle.<br><br>It results that the name of half of N2 molecules is changed as DUM. (maybe the system become neutral)<br>The number of N2 molecules should be fixed. <br>Do I have additional N2 molecule for charging using genion?? Then, what are the initial coordinates???<br>
<br>please help me....<br><br>any advises would be helpful.<br>How can I do that??? <br><br><br>