Dear Prof.
May I ask you two questions, Please?
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:
Volume = 1000 nm3
Density = 15.8111 gr/l
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:
151 * 5 = 755 beads ( since all particle masses are set to 72 amu in MARTINI ),
then 755 * 72 amu = 54360 amu,
and 54360 amu / 6.023*10e+23 = 90254.026*10e-24 gr
then, density = 52.23 gr/l but the Gromacs gave 15.8111 gr/l!!!
And there is the same problem after adding water and ion!
May I know my mistake, Please?
2- My surfactant molecule has one positive charge, after I added 151
surfactants, water and antifreezewater, Gromacs answer me that (for each step):
NOTE1: system has non-zero total charge: 1.510000e+2
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?
Please help me.
Best Regards
Sara
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