On 15/12/2011 5:59 PM, mohammad agha wrote:
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!!!
Please use standard abbreviations for your units unless you want risk
people not taking you seriously...
I've no idea how you can divide 90254.026*10e-24 by 1000*10e-24 and get
52.23 or 15.8111
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"!!!,
When did genion report that, before or after adding ions? Did the
addition succeed? Are your solvent molecules named "SOL"?
but after doing grompp, GROMACS didn't report "note" about system
charge. Is this right?
We don't know. Copied and pasted command lines and terminal output are a
lot more useful for getting help than sentences describing them.
Mark
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