<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div><br><font face="times new roman, new york, times, serif">Dear All,</font></div><div><font face="times new roman, new york, times, serif"></font> </div><div><font face="times new roman, new york, times, serif">By gromacs pdb2gmx, we can choose the amber force field. Suppose we have chosen the amber force field, now let us see add ions.</font></div><div><font face="times new roman, new york, times, serif"></font> </div><div><font face="times new roman, new york, times, serif">By gromacs command "genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral -conc 0.1", besides neutralize the system, we also add 0.1 mol/L NaCl to the system.</font></div><div><font face="times new roman, new york, times, serif"></font> </div><div><font face="times new roman, new york, times, serif">For AMBER, the comand
to neutralize the system is as following: <font>addions dna1(or some other name of the system) Na+ 0 or addions dna1 Cl- 0</font></font></div><div><font face="times new roman, new york, times, serif"></font> </div><div><font face="times new roman, new york, times, serif">From my knowledge, in AMBER there is no command to add a certainm concentration of NaCl to the syste. But in its mdin file of the AMBER, we can specify "<b><font>saltcon=0.1</font></b>", which means salt concentration is 0.1 mol/L. As I have not tried, my current knowledge is that there would be no 0.1 mol/L NaCl added to the system by AMBER, but it will calculate as if there is 0.1 mol/L NaCl.</font></div><div><font face="times new roman, new york, times, serif"></font> </div><div><font face="times new roman, new york, times, serif">Then may I ask, for using AMBER force field by GROMACS, besides we add 0.1 mol/L NaCl by the command "genion -s ions.tpr -o solv_ions.gro -p
topol.top -pname NA -nname CL -neutral -conc 0.1", shoud we also insert "<b><font>saltcon=0.1</font></b>" in the gromacs mdp file?</font></div><div><font face="times new roman, new york, times, serif"></font> </div><div><font face="times new roman, new york, times, serif">I am looking forward to getting a clarification from you.</font></div><div><font face="times new roman, new york, times, serif"></font> </div><div><font face="times new roman, new york, times, serif">Cheers,</font></div><div><font face="times new roman, new york, times, serif"></font> </div><div><font face="times new roman, new york, times, serif">Acoot</font></div><div><br> </div> </div></body></html>