<html><body><div style="color:#000; background-color:#fff; font-family:verdana, helvetica, sans-serif;font-size:12pt"><div>Dear Prof.</div><br>May I ask you two questions, Please?<br>1- I work with MARTINI force field. I have a surfactant molecule consists of 5 beads. After I placed 151 surfactants into my simulation box (cubic) with length of 10 nm, Gromacs reported:<br><br>Volume = 1000 nm3<br>Density = 15.8111 gr/l<br><br>My volume is right: 10 nm * 10 nm * 10 nm = 1000 nm3 = 1000*10e-24 L, but about density, I think that I am wrong:<br>151 * 5 = 755 beads ( since all particle masses are set to 72 amu in MARTINI ), then 755 * 72 amu = 54360 amu,<br>and 54360 amu / 6.023*10e+23 = 90254.026*10e-24 gr<br>then, density = 52.23 gr/l but the Gromacs gave 15.8111 gr/l!!!<br>And there is the same problem after adding water and ion!<br>May I know my mistake, Please?<br><br>2- My surfactant molecule has one positive charge, after I added 151 surfactants, water
and antifreezewater, Gromacs answer me that (for each step):<br>NOTE1: system has non-zero total charge: 1.510000e+2<br>Then I added 151 ions to my system with -nn 151 for neutralization, but in the genion.log was reported that "System total charge: 151.000"!!!, but after doing grompp, GROMACS didn't report "note" about system charge. Is this right? <br><br>Please help me.<br><br>Best Regards<br>Sara<br><br><div><br></div></div></body></html>